We prefer staying downtown... much more life there, the marina area is VERY quiet apart from party night [Friday]. The first time we visited it was party night and loved the atmosphere. We then went a few days later to eat and found it like a ghost town and a real let down of us.
Getting about is no problem. I believe there is now new tuk tuks, £1 for two and also a new bus [brighly coloured and not open like the other ones, so hair not ending up like a birds nest after a journey!!!!!] These are running aside the old services. Also sea taxis. Taxis are very cheap, and you dont have to haggle, dont know current price.
We cant wait to return, staying a bit further out this year, Steigenberger, great hotel and amenities and know that transport is no probs, bus runs every 15 minutes during day and evening for just over £1 pw, and only minutes away from downtown, and a bit more to the marina. Best deal we have had in a long time
Whatever you choose you wont be disappointed!