Well since it says fan favorites, I'm not gonna talk about things like pikachu and the pikaclones, since I perceive that the term "fan favorite" does not apply to these in the slightest. I know very little people, as a matter of fact, that isn't either "meh" or "gosh" about them. On the other hand it is true that most of the people that are not into pokemon pretty much only remember the franchise by pikachu, bulbasaur and charizard, all mons heavily featured in the anime from my childhood times (at least that I know of). That doesn't mean that these mons are fan favorites either, because if these people I'm talking about are not fans in the technical meaning, but just know what pokemon is from these widely featured mons, then they can't be called "fan" favorites, or at least I don't intend to do so. Is like these people that say "my favorite mon is pikachu" and the only mon they know pikachu; no wonder it is your fav then.
Anyways, let's start with one that has appeared a lot here already: Charizard. Gen I starters are far from holding a special place in my heart (most starters don't anyways), if anything only bulbasaur holds any charm to me from these 3. Blastoise I find bland other than the interesting fact its anatomy includes cannons and then there's Charizard. Everybody knows charizard. Everybody loves charizard. Charizard is OP. Well no. Not quite. I never really understood what kind of charm does this non-dragon dragon have to make it so that everybody I seem to meet in real life that knows what pokemon is thinks that Charizard is the best starter ever and that from Turtwig onwards everything is crap or just "not as good as charizard". Well I can understand nostalgia MIGHT play a big part on this, given that I wasn't around when everybody was playing their 1st generation pokemon games in their nintendo machines, the ones I couldn't afford. But nostalgia is sometimes a big threat: it makes you remember things way better and way cooler than they might seem to you now that you've grown, just like it happened to me and some toys I had when I was a kid. I'm not saying, however, that you just can't genuinely like charizard, or that liking it over everything else makes you a genwunner (gengwunner? gengoner? whatever). Liking charizard is cool, I like charizard, just not as much as other pokemon, but that isn't bad either. Is just that there ARE people that will defend charizard over everything else that exists, be it same gen or not. And I find those people boring. That's all there is to it, is not the pokemon itself as much as it is the people that will try to make it be seen as the OP pokemon that it isn't, even if it means only talking about charizard. All the time. Ugh.
Oh, there's also the thing GF did with this thing's mega. Or should I say, megaS. They were very clever IMO, killing two birds with one stone: first, that using two completely opposing designs instead of a single one considerably reduces the amount of charizard fanboys that will get butthurt with them (if they only went for one of them, either X or Y, they were risking to have one part of these people not giving them more money...), and second, that making one starter have two megas where others have 1 or none, is what a charizard fanboy will receive as the "finally the love he deserves!" love-letter from GF. They weren't playing games when they decided to give this thing 2 megas, and from a business point of view, they're smart sons of guns. From my personal point of view, is just unfair towards other equally or non-equally loved starter pokemons that deserved the stat push of a mega as much or more than charizard, but got nothing instead. This also applies to Mewtwo, who got two (considerably worse-designed than the original IMO) megas for pretty much the same reasons charizard did.
I don't have many others that I haven't mentioned already somewhere else for different reasons: garchomp, rayquaza, salamence.... all the mons that are already crazy powerful and loved by "everyone" and yet still get a mega, just so that GF makes sure these fanboys will keep on giving them money....ugh. Neither of you guys deserves a mega as much as little guys like marowak do, and yet I still would like a genuine evolution, but since we're in the mega-wagon, at least let me have weak mons get some love. Don't make things 60 stat points more powerful than God, that's the only rule of thumb that, if followed, I wouldn't even care if they gave a mega to everything. But then mons with 760, 780 BSTs appear.... and yeah, unless they re-make arceus as a 150 in every stat thing....the whole mega business will only scalate, I'm sure of it.