If I was ordering a brand new boat from the factory and they asked me which motor I wanted to get between the F225 and the F250 then I'd definitely strongly consider, and very much likely say the F250. Especially if the difference in the price between the two of them is minimal, if they actually had both motors in stock ready to go and so forth as I think the added up front extra costs would be very much justifiable in the long run. If I was in the OP's shoes, or even my own, and was repowering a boat right now and both Suzuki DF225's and DF250's were ready to go and available, I'd definitely consider and probably even splurge the extra money to get the better performing motor, especially if the price difference between the two was only a couple thousand dollars more. That being said, I personally wouldn't want to wait the 6 months just to get the better performing, more expensive motor just to get a few mph more out of it and save a few extra bucks on fuel at the dock.
I also wouldn't, and didn't, pass up on a used 228 Seafarer just because it had an F225 on it as opposed to an F250, and I personally don't think it would be worth spending the extra $25k+ to re-power my used boat with a new F250 just for the extra power when my motor runs great right now. At least that's my opinion and for my particular fishing/boating application it just doesn't make any sense for me to do when I only bought my boat for just over $25k to being with. In the OP's situation where he's also going to be spending more and waiting for 6 months on top of that? That would be a deal breaker for me personally, and it kind of sounds like it is for the OP as well in that he doesn't want to have to wait the 6 months. And I don't blame him, I wouldn't want to go all of June, July and most of August waiting on a motor that costs more money and goes a few mph faster to where it also would severely impact the amount of days I can fish by half, at the very least. If the DF250 was ready to go today or even over the next 2-3 months then I'd definitely consider it a bit more and maybe even go that route. 6 months is a fair amount of time to wait, and I can't imagine that that's etched in stone, because 6 months could come and pass and they're still backordered or delayed, behind schedule or so forth. Just my opinion, of course though, it's the OP's boat, decision and money... the choice is ultimately up to him and what he wants to do.