Many divers go to Sipadan simply because of Sipadan and nowhere else will do.
It must be boring being so myopic!
Other than the fact that the season is wrong for both Sipidan and Bunaken, I find this beat up over the Sipidan permits, well a bit of a beat up. I know because I too was stressing about the before I went. The simple solution is to book with one of the day operators with accomodation on Mabul, rather than one of the resorts. I think Scuba Junkie has the most solubrious accom of the day operators - nice clean cottages with A/C and hot water. Lovely reef of its jetty, crytal clear water with mandarin fish at dusk. Comfortable communal area and a limited bar upstairs. It is also right next to a local village so you can hang out with the kids. We got 1 day at Sipidan for every 2 days diving at peak season with no issue. And I found I loved the diving around Mabul and Kapalai. It was just as spectacular as the diving at Sipidan. Just different. Having the variety is excellent.
December/January is time for R4 and Similans. However, on the last trip to Similans (Jan 2010), the coral was in pretty bad condition due to a coral bleaching incident. The Thai govt even closed down access to parts of the national park. Will be heading to R4 in November, so can let you know what it is like, but it is only another flight on from Manado.
All the best for your honeymoon where ever you end up!