My main beef with it is that Hypermode was horribly-executed. I don't like a cast-from-HP weapon in the first place, but it could have been much better if they had kept the beam-switching system, let you select the Phazon Beam as a regular beam, and only take health off for each shot you fire when it's selected, instead of using an energy tank whenever you just need a few shots, or, at the other end, instead of having to re-enter Hypermode when you need more firepower than one energy tank gives you.
Also, the atmosphere of isolation is pretty much gone, what with all the intelligent beings that aren't trying to kill you. If you can call the GF Troopers intelligent.