I think what I'd prefer to see would be new features not being taken out of games; it'd be nice if they kept adding new features to each instalment, but retaining all the old ones. There really isn't any reason for them to take them out, other than time constraints, and I would be quite happy to wait an extra year if it meant keeping them in. I suppose card capacity might be an issue as well, but in this day and age, patches and expansion packs exist, and there is no reason these can't be implemented in Pokemon games. We already have patches to fix bugs in the sixth generation; why not take that a step further and release patches with features added? Hell, even adding them as DLC would be better than not having them at all!
Pokemon might not be seen as so stale if they didn't keep releasing titles every year. Don't get me wrong, I'm happy with their work ethic here - I loathe waiting longer than 2 years for new games; delays are highly frustrating and the hype quickly dies away - but if the extra time would be what it took for them to deliver more content, I'd be happy to wait for it. Each year we get a new Pokemon game and, whilst some new features are added, some of the cool old ones are taken out, and it's disappointing, as sometimes the new features really don't make up for the old ones that have been taken out. It doesn't feel like a new experience; it feels like the one that preceeded it, only with a couple of small features added in or taken out. The only really fresh experience from Pokemon these days comes from exploring a brand new region. This isn't necessarily a bad thing, but sometimes I think they rush things a little and could make things much more interesting if they added more for us to do in the games, rather than taking out things we loved and then expecting us to love things they put in in their place, when they aren't necessarily as good.
I'd prefer it if they kept everything in. Not necessarily the regions - exploring every preceding region in every Pokemon game would be insane - but all those cool little optional extras, like trainer customization, the Battle Frontier, walking Pokemon, and so on. Build on the world and the experience, don't cut and paste parts of it out. The regions can have plenty of character if you put more time into telling the story and detailing the locations; gameplay features shouldn't define the region in my opinion.