Here's my take:
Priority 1 Priority 2
Improved sprites/ voices Online high score table
Improved level select screen Medal system
Multiple accounts system Level editor
Sound and music controls Challenge levels
Ending rankings Algorithm enhancements
It's pretty much an industry staple, that if you make any improvements to the graphics you should do it early on. That way, early adopters aren't "cheated" out of their money, because after a player invests 10 hours in finishing the game, he isn't going to revisit it on account of a graphical update. People revisit their games when new content is added. Hence, add graphics improvements early on, maintain a steady stream of content.
-The in-game sprites seem outdated in comparison to the new, highly detailed portraits.
-The level select screen needs a graphical redesign, and a clear and concise representation of the level's data. As for the graphical redesign I was thinking since the whole game is about path space, the level select screen can be a path onto itself, with nodes to represent the levels (think of a glorified Super Mario World level selection screen). As the path is revealed partially after each mission, the complete path can be the outline of e.g. the Danmaku point.
-Multiple account systems offer a level of professionalism without requiring any serious programming (so you should be able to get this in without breaking a sweat)
-Sound and music controls are important enough to include on the first patch. People don't like reaching for the volume control
-Ending rankings (time played, number of kills, favorite tower, most efficient tower). This is a very high incentive for the player to keep coming back to the game, with no major programming hurdles
The rest of the noteworthy features I've grouped into the "second" patch. Content additions aren't necessary yet, considering the game already features 100+ levels. You'll also better off ironing out the high score/ ranking system before you create an online high score table. As for the medal system, I have reservations. It sounds like an afterthought to me, but I haven't played FFT from which I gather you take inspiration.
Oh, and I don't think you should change the balance, *again*