My favorite FF is XIII (it's the first FF where I actually did a 100% on). I've played all of them except XII. X is a great FF on its own but equipped with X-2, it blows all the other FFs out the door along with their own sequels/counterparts. FFIX is my 3rd fave. VII is too overrated. IV and VI are where the true fantasy lies. V is good, VIII is okay. FFI is a classic so there's no argument there. FFII is probably by far the worst FF IMO. III is slightly better than II.
As for Pokemon, RBY are classics, full of bugs yes, but classics. Can't argue with that. GSC was a full scale upgrade and really just blew me away. Some consider them to be classics as well. RSE was okay but for many, it was the start of the newer Pokemon fans so its the standard for them. DPP was okay. Tons of things to do but had some flaws. I felt like DPP covered RSE flaws and RSE covered DPP flaws. BW/2 another start to newer newer Pokemon fans so its their standard. BW/2 definitely was better than RSE and DPP though. As for XY, we have yet to see. I didn't include the remakes because well, they're simply remakes.
The FF and Pokemon series are both equally my favorite series of all games so I can't decide.