Three weeks is perfect for a honeymoon, not to try and see SEA. Cambodia really is just Angkor Wat for most visitors. I don't think trudging around old rocks is what you want to do on your honeymoon. VN is great, but I think Tland has better infrastructure and options for you guys.
I would spend 7+ days in in the Chiang Mai (CM), Chiang Rai area. for some trekking and Thai culture. Overnight buses or fly. Nok Air flies this route at cheap rates. If you decide to use the bus system, use the gov't buses. All travel agents try to put you on the private buses that are for tourists. These buses leave from their travel shop or guesthouse area. You will be safer and have a better experience if you use the buses the Thais use. Go to the bus station and book it yourself. Morchit or Northern Bus Station services CM from BKK. Bus or fly back to BKK.
Now for some beach time. I already mentioned the Krabi area. Overnight bus from Sai Tai Mai or Southern Bus Station. Overnight bus saves one night accomm. and you get in early am, perfect for finding room. Or use Air Asia: BKK-KBV, about 1,500 baht advance purchase.
You have enough time to hit the beaches further south or take a bus over to Surat Thani and visit Koh Samui and Koh Phangan. You can fly back to BKK on BKK Air or use the overnight train or bus from Surat Thani. BKK is worth 4-5 days IMO. Several easy day trips: Kanchanaburi, Ayutthaya, might be worth your time.
Good luck with your planning.
[ Edit: Edited on 05-Sep-2011, at 11:46 by vegasmike6 ]