Re. Layering - it was fucking with the new engine so they decided to skip it to improve performance. They did the right thing, no point wandering around at 10fps for the sake of having whatever socks you want.
Re. Not being able to replay missions - the number of bugs encountered when they tried it was over 8000 and there wasn't time to fix it. This is mainly due to the eniviornmental changes that occur (blowing up the skyscraper, destroying/raising the bridges, increased/reduced gang presences, *THAT* island where the plane crashes). The guys behind the SR2 Gentlemen of the Row PC mod are trying to fix it and have confirmed Volition's reasoning for leaving it out is legit as they're struggling to get it working too but are hopeful.
Re. The Ho Boat's 'sell them/keep them' - yes, it's can be uncomfortable but i) for what it's worth, if you choose the latter Zimos goes on to unionize all Steelport's working girls; ii) the Boss is a fucking psychopath who does horrible things to plenty of people over the course of the three games. It's ridiculous to expect a vicious crime boss to be some kind of idealised 'Oh, they're a lovely boy/girl really, only hurt people who 'ad it coming and they loves their mum' 'nice' gangster figure.
Personally, my main problems are the Johnny Gat situation; the combination of that, trading up from a dope habit to a coke habit and the new VA leaving Shaundi pretty much insufferable for the entire game; some jarring/unclear storytelling (if you don't blow up the skyscraper and they don't tell you you're going to *dead person's* funeral, the way the Safeword mission starts, etc), the loss of Fuzz and the fact the antagonists are all rather weak and underdeveloped compared to the Brotherhood/Sons of Samedi.
Oh and the Boss going soft, though I guess it gets a pass as it's clearly a running theme of the story, coming up at both the start and in the final choice.