StarJeweled is my personal favorite of the three. The central complaint (from most people - and I agree) is that a best of five is too long. I think a good fix would be to allow voting over whether it should be a best of 5 or 3, as suggested by many players. I've been in some games were everyone either votes to quit after a winner out of 3 is reached, or just randomly leave at that point.
I haven't had any that took longer than an hour, but that's pretty long. Unless it's pretty one-sided (or somebody leaves) it takes that long fairly often. I personally think it's because of the back-and-forth nature of the game. Whenever one team makes a strong push, the other team can merely psi-storm it and start over. Strictly speaking it isn't IMBA because of the energy cost, but if used right it can set both players back to step 1. (Other things can cause this as well.)
Whether you agree with that I think the ability system should be changed. I had two ideas about this, the first being adding cool-downs. Not long ones, but long enough you could bluff the enemy with a mini-push and potentially make them waste a storm, and then release your full power.
On to the "bejeweled" part of the game: It works, and it's fun, but after playing it for awhile it gets a little dull. There are few enough ways to get 3 in a row that your brain starts to detect patterns that will get 3 in a row automatically, and sort of phases out. While a Bejeweled master could probably set the board up to get mega-combos, it takes too much time\effort for most players to do this. It's much better just to get them as fast as you can, especially since you also have to be watching the battle and using your energy. It would help to have more possible moves to add some depth too it. Maybe allow switching gems cornerwise or getting diagonal rows would work, but I guess this might break some Bejeweled Creed Rules or something.
You could spice it up without messing with the base game-play by adding special blocks and\or making the different block colors have additional special effects. For an example, spawning different units other than just marines depending on what blocks you used or providing minor buffs depending on the color used in the combo.
Special blocks would be the safest way to make the game more fun. They would be single blocks of specific color that, if used in a combo, would grant a special bonus. Referring back to changing abilities, you could make some of them grant ability charges. For an example, the special mineral block could have the Psi-storm icon on it and grant a Psi-storm charge.
It would make them think twice about using their abilities and it would be fun for the players to be awarded for concentrate on using these blocks in a combo.
Initially I thought the game play was really shallow because massing gems was better than deciding what units to get and casting abilities, especially since it seemed hard to keep the camera following the fight, and the countering system was different enough from ladder I actually had to read the tool-tips to figure out what to get. However, as I played more and got used to it I found it wasn't quite so true; smarter players can beat faster players. I still think it would be better if the countering system was more clear-cut though.
My final concerns: Tanks\Immortals tool-tip doesn't list any strong\weak points. I know this was intentional, but it seems to me that Ultralisks\Colossi\Towers could be listed under Strong Against and Air Units at least under weak against. Since they're heavy-hitters meant for towers, wouldn't zealots also be good against them?
Finally, (although this is very minor) it's a little bit hard to read the word “Starjeweled” in the preview image. Cropping down the surrounding blank space, making the text bigger, and\or making it have more contrast would be nice.