A very well thought out game, however there is room for some improvement. After I played through it the first time, I realized that speeding up the upgrade-points would be the best investment (At the end I had around 43 extra skill points). However, this does remove a lot of choice from the players hand since the game is otherwise harder if you don't put points into Skill point speed. I would suggest removing the upgrade for skill-point speed and making it so the upgrade speed increases for every skill point you research un-interrupted.
The weapon system also needs more refining since every weapon you get is clearly better than the last making switching weapons pointless. I would suggest having different firing styles which could include bullet damage, bullet speed, bullet spread, bullet amount, semi-automatic, automatic, etc besides just increasing firing speed, bullet damage, and magazine size.
Also, the skill-point drops seem too detached and random to matter, especially in late game. They act as more of a pleasant surprise than a true power-up. It would be better to add boss waves which could drop X amount of skill points so players can count on getting more skill-points besides through grinding the research station. Also, placing checkpoints after bosses would make sense.
Related to the research station, I felt that I wasn't making much of a sacrifice by using it in the first place, thus not making it feel like a choice at all (which is should be). Since the game is scored on how many days you take, being able to manually grow the plant would both give a player something worthwhile to do after they get capped on skill-points as well as make them have to chose how to spend their downtime to either increase their score or ease of play.
The power-ups that dropped were useful, but could be improved upon as well. Instead of activating when the player runs over them, instead they could be stored in an inventory of sorts that has a slot per power-up which could be mapped to the number keys. As a result the shop could sell power-ups which would give the player a place to put their money instead of just using it to become a god from the heal-purchase which always restores the same amount of health no matter what wave you're on. A good fix to this would to be to add a skill-point upgrade that would raise the life cap (possibly replacing the damage-reduction as well).
One last point I would make is that there really is 2 different kinds of monsters: Air and Ground. This results in a difficulty curve that is completely reliant on just sending more monsters at the player and as a result doesn't offer much challenge other than shoot. By add some monsters that launch ranged attacks, heal other monsters, or spawn minion-monsters it would stress the player more carefully chose where they shoot instead of just killing everything in sight.
All in all it is a very enjoyable game, but it's progression and challenge is too linear to give it replay value.