Improving, that's for sure!
First of all, the mixed bittages problem remains. I still think you should choose either 16-bit or 32-bit, as it looks odd when the bittages are mixed like this. I seriously can't stress enough how important this is! Especially considering how common the mistake is, which in the end only makes it worse! Rain effects could have had a TON more raindrops, expecially since the 3 or 4 onscreen ones only made it seem like a light drizzle with more sound than needed, which made it seem akward. Trunks' energy beam looked fine, but Sonic's looked a bit cut off. Also, it might have made more sense for Mario to have landed while he was stationary, rather than just floating. Styles were also mixed since Trunks was from a fighting game, but the others were from platformers. I suppose killing the ones who don't fit might solve the problem though, so... I'll just leave it at that.
Now, with the bad stuff out of the way, lets look at the good stuff, shall we? Blood effects were fine and detailed on the character sprites. The puddles weren't very good, but that can easily be fixed. After all, as I'm sure you know, blood is almost never in a perfect circle unless it's in a container, so don't just use the circle pattern when making it! Be creative in the puddle design, as you've already got the "bleeding body" kind of blood down! Also getting in some nice character development here, from Sonic's multiple expressions (nice tears by the way) to having Metal finally explain his motives for the audience. Trunks could have had a more detailed explination on his own motives (especially since chatting for a good while in common in DBZ), but for now it's fine without too much explination on his personality. Just be sure to get into his backstory eventually, as even villains need good character development, too. Sonic especially showed a good amount of depth in his character here, as while super he shows how he feels invincible and superior, but deep down is still a caring person, as shown by his grief and sadness from seeing Shadow die. I suggest having the rest of the cast socialize in the next episode about the whole ordeal, possibly their fears of the future, backstories, things to get us all to know them all better. After all, the cast of characters can easily make or break a story!
You've really improved this flash from the crappy cliche'd piece it started as, turning it into something that easily has the potential to be amazing! Might not be front-page material, but if you keep working hard at it, you'll soon have a flash series to TRULY be proud of! You could even use it as an example to young, aspiring flash artists to how well one can improve! But anyways, good luck in future installments!