I think it launching from your browser is the worst part. Some browsers really struggle with running plugins like that (FF3, IE6, Opera), etc.
Team Arena tried to make up for the things that went bad in Quake 3, it tried to turn DM into TDM and add on things that people liked from Q3 mods. If anything, it was aimed to improve the game for competitive use. It failed because the team command sucked, the bots couldn't understand the new features, the weapons were unbalanced, and about half of the maps were real crap and made to be walked in when Quake is all about running.
For all of the maps other than Q3CTF4, I think they did great justice to the maps by cleaning them up. So far all changes I've seen are either for balance or to fix glitches...except for Q3CTF4, it looks like they based it on the Q4 version of the map which makes no sense and is fail.
Navigating the maps hasn't changed at all and nothing is out of place, again with the exception of Q3CTF4 :x