I love this genre, and my passion for it has gone largely unsatisfied for a long, long time. The story is present and as good as it needs to be, graphics are good enough, sounds are good enough. +1 presentation.
In addition to having done the beat-em-up right, your additions are solid. Characters are in good variety, each have ever-expanding options for their moveset. I like sequences instead of hotkeys, but hotkeys are in style, so whatever. I definitely haven't seen two-layer customization of special moves in a beat-em-up, if any game at all, so kudos. +1 design
The AI-controlled henchmen, each with dynamic skillset, means that your character and skill build can actually be customized to fit a party together in different ways. I'm actually having a hard time finding a party composition that just won't work without fiddling with the skill particulars. +1 design, +1 execution.
Would have been cool to see character attributes evolving or buy or find equips in secret rooms, but there is a lot of character building going on anyway.
Enemies were varied and original. They weren't all pulled directly from a Tolkien novel (or any of the bajillion games that have done so) so I didn't immediately know the best strategy for defeating them. Figuring out what they were and how to kill them was often over before I could finish the process of trial and error, but hey, at least I didn't see an isolated village of elves who don't care for the cave dwelling dwarves who reluctantly came together to help me fight orcs with axes, and ogres with blunt objects all the time. +1 design, +0.5 execution.
The game is a little fast-paced for me to really evaluate sidekick and enemy AI, but generally when I play the role I put together for my character within my party, I encountered the challenges I expected, won if I filled that role effectively, and lost if I didn't. Therefore, the sidekicks and enemies must have all known what they were doing. +1 execution,
I felt that the hitbox width and character reach were a little small; for reach, go ahead and make the attack animations a little more dramatic than a quick rotate arm/skew body, maybe make weapons a little longer. I can't even count how many times I whiffed repeatedly thinking surely I was in plane and within a sword's length. I did get used to it, though, so just -0.5 execution. For the fact that I often couldn't tell whether my character had actually done his or her skill animation or if instead I had slipped my finger and just attacked normally, I have to dock you -0.5 presentation too.
A lot of folks have complained that there is a lot of frameskip type lag. I didn't see this as game-breakingly bad running FF on Win7, computer maybe 4-5 years old that was not at all top of the line at the time. -0.5 execution.
The lag is what I call frameskip because it appears that time elapses even though it is not being drawn or accepting input. That means some threads of your code maintaining the game state are performing fine, but some step limits the rate at which the state can be rendered. I don't know a thing about flash, but if I was writing this for HTML5, I would rule out any physics, collision, mechanics, and AI as optimizations and focus on graphics and layers close to it. The circumstances I saw where there was some lag involved having a lot of enemies running around (i.e. the necromancer before I realized he was summoning more mobs) or a lot of status effects or other special effects going on. Obviously you'll want to limit the number of active characters - I do hope that necromancer boss has some sort of limit, and if so I think you should turn it down. If you haven't been doing so, some of the enemies and some of their animations can be pre-rendered to make them draw faster. I don't recall if they did any really dynamic stuff like ragdolling, but you can rasterize and cache just about anything else. This will be especially helpful if your textures or sprites are getting scaled down or rotated all the time. As for special effects, you always have to watch out for a lot of dynamic transparencies - especially dynamic radial gradients. Remember that these can be rasterized too, and while composition will still cost you, at least you won't be doing so many square roots on every frame. When I did this for 5ong (RIP) there was no perceptible quality loss and a truly epic performance improvement.
Just two other bugs bring your total down from 5 stars to 4.5. At some point (I'm gonna guess after I lost a battle then tried it again) the "Game Over" screen started to fade in over the battlefield every time I paused to use an item or fiddle with skills. The game didn't end at that point, so no big deal, just weird, -0.25. Finally, I often had to cycle through my whole party - I think several cycles at least once! - at the beginning of each battle in order to be in control over the character I wanted AND have the correct skill bar displayed. Again, no big since there wasn't usually an immediate ambush, I got used to mashing F a few times at the start of each battle, -0.25.
Your final score of 4.5 means that you have made a great game with a few pesky flaws that will not prevent me from finishing it and having good fun doing so. Probably right now. So cheers!