I'll be updating this review with more thoughts, but some things were made better in the first version. I have to say that I am not praising this game like most of the people. Few things so far:
1. Not being able to stay in the full screen mode if you want to pause the game and restart it. Pressing escape makes also exits full screen mode.
2. About multiplayer and alternate controls scheme: using right-click for anything has to be changed, because right-clicking in Firefox disables the keyboard. The game should be fully functional for all browsers.
3. The description of the NG medals should include all the requirements that have to be met. Hovering over all of the ? boxes in the in-game medals section just to find a certain medal is a bit annoying. At least it would be better if the medal icons were grayed out until unlocked.
4. As for some medal requirements: a bonus round is a bonus round, so it should not count.
5. Changing the normal upgrades system into a system based on purchasable cheats is a bad thing. And having to purchase the handicaps is a bad thing as well. Having a traditional upgrades system makes it possible to create levels with much more variety of fair difficulty.
6. I admit I am not necessarily a fan of bullet hell games because of one thing: after some time of playing and heavy focusing on the screen it always makes the eyes unnecessarily tired, especially when you have to dodge tons of flashing bullets. It's simply unhealthy.
7. On the other hand, positive this time: a pacifist mode is an interesting thing to try, it actually helps you understand the patterns much better than playing a level in a traditional way.
A PS to your concern:
As you probably know on Newgrounds flash games are not going to die thanks to lots of effort made by PsychoGoldfish and TomFulp. Besides, there are still many ways to keep playing flash games anyway. I wouldn't be so sure about the sponsor of your games Kongregate though since they are "re-profiling" and flash games actually can be dropped by them.