Simply put, this isn't a real important issue. The number one reason for my arguement is that all RTS games, such as Starcraft and Warcraft have their main and bulky UI on the bottom of their screen, and use the exact same game-types and camera angles. While sure, Warcraft had a turn camera ability, it only made things worse than they were.
Then you have the game this was based off of. The exact lay-out and style with some minor changes. Never once have I heard any complaint that the team on top had to battle with the UI. Granted the exact execution of skills and functionality is slightly off, if you're competent with mouse-movement you'll be able to play just fine. Granted I myself have even typed in the fame "BS!" from clickin' on the very edge of the UI, makin' my thunder shuriken fly off to my NW, missin' the killing blow entirely... I haven't ever really be beaten by it, or had it cripple a game. I compansated for it the moment I made the mistake the first time.
In conclusion: It's not a game-breaking design, and it doesn't interfere with the the individual games, giving help to one team while ruining the other. It's a minor flaw that comes with the territory.