I know that when our market was really hot it was harder to get FHA loans accepted, but we still got FHA offers accepted often. especially now with the market slowing down a bit its way easier to get them accepted. If it makes more sense to do FHA because its only 3.5% down and that's best for you tell your lender that. The hoops that the sellers have to jump through for FHA are just in the conditions of the house. FHA requires that there is no peeling paint on the property, there has to be a certain amount of years left on the roof (I don't remember how many though), no major hazards.
Your realtor where you live should have a pretty good idea of what things the Appraiser would call out and ask for the seller to fix those before the house got appraised. shouldn't be too big of an issue unless your looking at houses that are in need of major remodels before they are livable.
again my Area is most likely a little different than yours and your agent should be knowledgeable.
Do you have a realtor you are using where your living?