If you consider only the price aspect, since you've said that's a concern, North Sulawesi offers many choices of dive ops and lodging at every price point imaginable. You have a mix of walls and hard corals at Bunaken, excellent soft coral diving at Bangka, and one of the world's premier muck diving destinations at Lembeh. Your travel will "probably" be easier, shorter, and less costly to Manado. This, of course, varies with your routing. And no liveaboard ($$$$) required to dive all of it.
In my opinion, while RA and Komodo bear a lot of similarities, neither of them compares directly with North Sulawesi, though if you consider that you have three separate and distinct dive areas available there, you're not going to run out of first class diving. Between boat and car shuttles, and many dive ops competing for your rupiah, you hardly have to miss a dive if you want to do a couple of resorts.
RA, Komodo, and North Sulawesi are all great dive destinations. As a
generalization (yes, you can find exceptions), North Sulawesi will give you the most varied diving, with the most flexibility, at the lowest cost, IMHO. Now I'll sit back while everyone proves me wrong.