You can keep running F3 for the time beeing, later on you can move to Aurora if you like, or you can try it out now... however, keep in mind that it's an Alpha, so bugs are to be expected...
Yes, it's possible to replace F3 with whatever you want, but tbh... there isn't much to "update" what really needs updating is to add new features and/or fix bugs...
There are no compatbility issues with any dashboard afaik, the only compatibility issues is that XEXMenu and other older loaders don't support GOD...
GOD's will work just fine with any new dashboard made these days...
Aurora is simple and it works very well with all the features that are implemented, there have been very little major bugs with it, but then again, most of the guys in Phoenix were part of Team FSD