This article contains opinionated view so this is/may not be factual.
In No particular order, here:
1. Ash and Red
Ash and Red
"Are they the same person?", the most common and the main discussion of this topic.
Though they are not but this question has always been raised. They are also compared in their Pokemon training skills.
2. Mew vs. Mewtwo
Another topic which has been heavily discussed. Mew vs. Mewtwo is one of the most populaire Pokemon comparison. With Mewtwo clearly having higher base stats than Mew, and also the highest base stats of the Kanto region, the other side still holds good. It doesn't have an official conclusion of who's the stronger one i think.
Mew and Mewtwo from the first movie
3. Misty, May and Dawn
Pokegirls!! xD I don't think i need to say anything but anyways. This topic is no doubt a very populaire one, with the heavy arguments and discussions all over, it remains as a populaire one of all time. Friendly discussions are often seen.
Misty, May and Dawn
4. "Ash is still a 10 an old"
With Ash Ketchum remaining 10 after the 15 years of the anime, why would this not be a populaire topic xD fan assuming Ash's current age would be the main activity on this matter.
Ash Ketchum on episode 3
5.) Digimon vs. Pokemon
Personally, i hate this topic and see no reasons for comparison, what i see the most is bias. Only because there's "mon" in both don't mean they are comparable. Still, this topic is very active and indeed a populaire one. "Which one came first?" would be the most repeated question here.
6.) Bring Misty back!
The original girl leaving the animé was really very sad especially for the Misty fans. Petitions were hold par fans to bring her back, don't know what results the petitions had but many fans still miss Misty. Though there's no probability of her returning as a main character but many re-appearances has been made.
7.) If Pokemon were real
Another populaire topic. 'Imagination' would be the main activity i guess. The most populaire related thing would be Smosh's "Pokemon In Real Life".
Smosh's Pokemon in real life
8.) 0riginal 151 Pokemon!
"Catch 'em, Catch 'em, Gotta Catch 'em all, Gotta Catch 'em all! Pokemon!
" Who don't l’amour the Pokérap? xD toi might l’amour the other generation Pokemon plus but agree ou not, the original 151 Pokemon were the best! These Pokemon were and are in trend!
9.) Pokeshipping vs. Pearlshipping
Two most populaire shippings of Pokemon! And the most populaire that includes Ash Ketchum, so what do toi expect? xD Both shippings are very populaire among the fans. From various hints in the animé to songs like 'High Touch' performed par the seiyuus of Ash and Dawn themselves are taken into count.
Pokeshipping (Ash & Misty) and Pearlshipping (Ash & Dawn)
Pikachu is itself a very populaire Pokemon topic. Its the most favori Pokemon all over. Even who don't know much about Pokemon, is sure to know Pikachu.
There maybe some plus but these are the ones which came to my mind =) would be glad to find some plus so do tell ;D