I don't think Anya suffered as much as the others, but I agree that they were definitely left out a lot of the time. Anya basically showed up as comic relief most of the time, but the others got the shaft for the majority of the season.
If I had been given creative reign over the last season, I wouldn't have brought in all those Potentials. I admit, I thought the Potential storyline was cool, but I thought it would have made a much nicer plot twist to have Buffy be able to choose who she could share her power with, and give some of it to Giles, Xander, Dawn, Anya, and Willow so that they could have been the ones with the power after the spell was done, or at least been part of the ones who did.