Fuck bubbles, but more on that in a moment.
PROS: While in the style of Pokemon, it feels different enough to keep me interested. Some of the monster designs are nice, and the skill tree system is a nice addition that allows multiple copies of the same monster to still be unique; you can even dip into more than one tree once your get enough talent points! The animations, music and sound effects, while nothing stellar, do their job well enough, and I've never felt like I absolutely HAD to turn off the sound. Gems are something else I like, taking the place of Pokemon's hold items, and you can have up to two (one more is unlocked by visiting sogood.com, while the other is unlocked by... I'm not sure, actually. Reaching a certain level?)
CONS: What should be a fun game is brought down by questionable decisions. For starters, there is no on-demand way to see how each Type fairs against one another, leading to a lot of guesswork.
--There is no way to tell if something can evolve except by leveling them up and filling the Monsterpedia; Pokemon is guilty of this as well, but that doesn't make it a good idea.
--I'm not sure if the Taunt passive works properly; it SHOULD be that each monster with Taunt will take a percentage of the damage the intended recipient would have (ex: Mon-A would normally take 100 dmg, but Mon-B has Taunt+45%, so Mon-A takes only 55 dmg and Mon-B takes the other 45) (ex2: Mon-A would take 100 dmg, but Mon-B has Taunt+45% and Mon-C has Taunt+30%, so Mon-A takes 25 dmg, Mon-B takes 45, and Mon-C takes 30), but from my observations that isn't how it works out.
--The most important stat is Energy, which takes the place of PP in Pokemon, or MP in Dragon Quest Monsters. If you run out of Energy, you are forced to use "Desperation," a typeless move with 20 power that shaves off 25% of your health AND does 10 dmg to you. This is a bad thing, so you'll want plenty of Energy. The problem is that some monsters have absolutely pathetic Energy levels in comparison to their moves' costs, resulting in some attacking maybe twice before being forced into Desperation. This is WITHOUT taking into account an overpowered debuff that reduces your max Energy by 25%, stacks as much as desired, and never goes away once applied except with a move that clears debuffs. Said move is usually found in a skill tree comprised of mediocre-to-bad moves. Expect to see plenty of enemies abusing this to render your monsters incapable of fighting back, especially as you progress.
--The skill trees are not balanced. Every monster gets three skill trees; the one on the left is usually damaged-focused, the middle tanking/healing, and the right support, with the first two being based on the monster's own Types where applicable. The right tree is USUALLY borderline worthless because most of the moves are usually Normal-type, meaning they're effective against Holy, a Type that is quite rare and usually is paired with another Type that gives it a more common weakness ANYWAY. Some monsters have really good setups for their skill trees, while others seem to get the shaft.
---For example, the Holymantis (Plant/Grass)'s first skill tree is "Grass," focusing on healing. Its second skill tree is "Holy," which also focuses on healing. You would EXPECT one of them to be single-target heals, while the other is multi-target, balancing out the group heals with larger costs. INSTEAD, both of them are centered on single-target heals, but Grass' heals apply Heal Over Time effects, making them more useful. Holy, meanwhile, offers some overly expensive single-target heals and some fairly weak damaging moves. Woo.
-As far as I can tell, there is only one offensive stat, which is Attack. If a monster has a bad Attack stat, and is loaded with raw damage moves in its skill tree, it will not be very useful. I also don't have any idea how damage calculation works, so that may be an issue as well. This is also an issue if the monster's main form of offense (like the aforementioned Holymantis) in one of its skill trees is through Damage Over Time effects, since they can be unreliable by, say, a bubble.
-While there are seven or so tiers in Gem strength, the numbers they provide actually varies, resulting in things like a Tier 6 Health Gem granting only 17 Health, while a Tier 3 Health Gem grants 12.
-You felt the need to introduce monuments in battles that alter how they work; this is not inherently a bad thing, since it can prevent monotony. HOWEVER, not only are they most of the time unfairly stacked against the player, but some of them seem specifically designed with the intent of making the player want to kill themselves. One type of monument counts down from a number, and when it hits 0, automatically uses a move for that side. I recall one trainer where the monument for my side was +15% Speed, and the enemy's side was a 6-turn countdown to the automatic use of some move that depicted a flame-engulfed tyrannosaurus head. Once that countdown hit 0, it would randomly hit one of my guys, say "Not effective," but one-shot them ANYWAY while ALSO one-shotting my two tanks with Taunt, because balance.
--Another type of battle condition is resurrection; when a monster dies, a tombstone appears and they will revive with 50% HP after 12 turns. In one case, the enemy side was the only one that got this benefit, and I got absolutely nothing.
--By far the absolute mot ridiculous, obnoxious, infuriating of the monuments, however, is the barrier stone. These stones render 1, 2, or 3 monsters (depending on no. of monsters) on each side completely and utterly invincible to everything, removing and reapplying themselves to random monsters at the end of each round. Your tanks cannot use their Taunt passive to absorb damage if they have a bubble. DoT effects do no damage if the monster is in a bubble. You want something dead that got a bubble at the start? You're just going to have to target something else! Enemy monster you got on the verge of death lucked out and got a bubble? Better hope the enemy side doesn't have a healer! Enemy healer got a bubble? Better kill what you want to kill in one turn, before it can heal them! Rely on your Taunters, as the game flat-out says you should, to mitigate damage to your squishies? Boy, I sure hope your Taunters don't get a bubble! Every time you see a bubble monument after the first one or two times, the enemy teams seem specifically designed to take full advantage of it, changing the fight from "difficult" to "bullshit."
-Every four levels of the tower you run around is essentially a Pokemon Gym, all centered around one Type (Plant, Fire, and so on). YOU WOULD EXPECT the trainers within to use monsters of that Type. After the first two, the trainers apparently decide "fuck that shit" and proceed to use things that don't match their Gym's Type at all. Now, the second Gym uses a few Earth-Types, but they're weak to Water just like Fire is, so it's not too big of a deal. The third Gym is Electric, but you won't find any Electric-Type monsters for the first two or so levels - only Robot, Ground, Grass, and, for some reason, Water. This is a gigantic middle finger to the player by arbitrarily changing the rules and expecting them to just go with it, especially since the next Gym (Undead) for the most part actually uses the Type it's supposed to.
-The game in general is schizophrenic with its difficulty; some levels are just right, some are laughably easy, some are hard, and then you have the ones with bubbles with impossibly-high Speed teams spamming area of effect attacks that kill you before you can even move, all the while mocking you with the "Not Effective" message. At times you find yourself having to level grind, which gets boring since EXP seems rather low, and it won't help until you're about five levels higher than the enemy.
-This is a minor nitpick, but I feel you should allow the player to choose from a number of monsters to start with, instead of forcing them into the cat and the pig. I never found the cat useful, and the pig stopped being all that great after the second Gym, even after reaching its third form.
FIXES: Monuments: Remove any and all bubble stones. There is no benefit whatsoever to keeping them, unless you genuinely want to piss people off, which I don't recommend. I'm unsure what to do about the move-use monuments; at the very least get rid of the ones that unleash some crazy powerful attack that will obliterate your monsters regardless of resistance.
-Gyms: Make the trainers actually confirm at least a little bit to their Gym's Type. I should not be seeing, for example, an Electric-Type monster in a Fire Gym, and I do not mean the pig you start with.
-Energy: Make the Energy debuff only reduce it by 10%, or 12.5% at most. It can still stack, but it should not be able to completely shut a monster down in one round unless the entire team is devoted to it.
-Skill Trees: I feel some of the headache could be eliminated by simply allowing monsters to learn some moves as they level up in addition to gaining points to spend in their trees.
-Gems: Reduce the range to which the Gems' values vary. I shouldn't be seeing a Tier 6 Gem give only slightly more of a stat than another Gem half its level.
-Need to Level Grind: The only thing I can think of is reducing how much EXP is needed to level up.
With all the above said, I hope to see improvements made, as you have a quality game, here - it just needs ironing out.