Personally, I find the stock Samsung roms to be perfectly good. I've rooted my S3 and disabled a lot of the built-in Samsung apps, but apart from that, it's still running the latest official Samsung firmware. It does everything I want, so I see no reason to change for the sake of it. (In other areas/devices I'm an incorrigible modder, so this isn't just apathy, this is the 3rd party roms not being compelling enough to change).
If I still have my S3 in a year or so when Samsung have stopped releasing updates for it, then I *might* consider flashing a 3rd party rom, but by that time I'll probably have upgraded to the Galaxy S4 or S5 or whatever the new hotness is anyway.
So, no it won't affect my decision, and I doubt I'm a unique case in this regard.