If you have a problem with the sound output, I don't think there's real difference between programs. Possibly the default EQ settings are not what you prefer, so play with them a bit. You can play around with different output plugins if you want (directsound vs. waveoutput).
As for the path that ripped songs end up in, well. To set that, you have to go to preferences and look at the CD Rip settings .. To be honest, it's the first place anyone should think to look and the place where it makes sense so I can't say I agree with this complaint.
The problems I quoted are not real problems with Winamp. They're only problems because you don't know the program. Still it's not hard and it honestly shouldn't take anyone more than a minute to figure out. I've never had an ipod, though. I know Winamp has support for it, but I don't know how well it works.