It depends on how adept the people doing the chips are and what they have to work with. OBDI vs. OBDII hardware, theres nothing on an OBDII car thats any worse than OBDI. Same size air meter, same general intake, cams, etc.
OBDII is a much more complex system. Thats not as bad as it sounds, if the system has been throughly figured out by the aftermarket. All of the extra stuff an OBDII processor has on it CAN let you tune them for extremely high HP if you have the tools. For instance, I would much rather build a high HP Ford that is OBDII than OBDI. The OBD I Ford stuff I dont think twice about dumping for a standalone. The OBDII Fords have ECU programmers that let you do just about everything you can do with a basic standalone except get rid of the MAF...I can datalog more ECU stuff with an OBDII Ford than I can with a TEC-3
BUT, if the VW aftermarket hasn't cracked the system that well, its all a bust..hahah. And Im not sure how well thats happened. Most of the VW aftermarket for ECUs seems to be about 2 steps ahead of where the American chip tuners were in 1990....About the only difference I can see between chips for a Mustang in 1992 and tuning an OBDII VW today is some datalogging and for the late late model VWs flash tuning pre-built programs...
Maybe by 2015 VW owners will have the ability to retune the VW ECU on their own laptop.....(and dont tell me about Lemiwinks)...