Since this is "top favorites" and not "better" it makes things easier for me. I will divide into two top 5 to cover the 2 series, since my top favorites are all on NPoT and leaving PoT out would be kinda bad I think ?
Prince of Tennis:
No. 5 - Ryoma vs Akutsu
If I remember correctly this was the first good match for Ryoma, that really demanded him, and Akutsu has one of my favorite playstyle in the series.
No. 4 - Tezuka vs Sanada
This one is the only match that I was really waiting in the finals, and then we have a beginning with Zone starting to waver, -> Hyakuren rendered useless, Saiki rendered useless and then the phantom. The techniques that Sanada used are also really good here and this could be the best match visually speaking.
No. 3 - Tezuka vs Atobe
Well, I don't really know what to say about this one, it's just you know, I can't really put in words here (even though I can't really put in words the most part of this list), it was this match that put Atobe as one of my favorites characters, I guess this enters here by the phrase "the first time you never forget" seeing as this was a first top level match on the series.
No. 2 - Yuushi vs Momoshiro
Now this is strange I know but I really liked this one, the playstyle that Yuushi use is simple yet I like maybe too much and Momo using his nature oriented Insight was probably the best point in the match, how calm he was, using the wind, the sun and thinking ahead. Then Yuushi counter Momo Insight to win the match like a boss.
No. 1 - Shiraishi vs Fuji 
In Prince of Tennis my favorite playstyle was always Shiraishi Bible Tennis, playing perfectly was simple yet... perfect
but seriously, Shiraishi countering all Fuji's counters and then Fuji evolving his counters and creating a new one (that I particularly liked the most) and even after Fuji's "evolution" Shiraishi yet managing to win, really hit me in a good spot. But this is probably in no. 1 only because I always had a hard time deciding who was my favorite character between Shiraishi and Niou (not anymore though).
And I think it's pretty astonishing that in this top 5 there aren't any Niou match even though he's my favorite, I could put his doubles agaisnt golden pair or his match against Fuji but I don't think I liked those that much compared to the five above, but in NPoT this changes.
New Prince of Tennis:
No. 5 - Niou/Atobe vs Ochi/Mouri
Here we got Niou doing a show, first we have a Atobe-Tezuka doubles (which is cool), a lot of service aces and Niou making the sacrifices for the win, after that Atobe is basically forced to play alone agaisnt 2 HS and what Niou can do to help is use an ilusion of Atobe to force a synchro and help Atobe to see what the enemies are gonna do and seeing your favorite character like this have some plus, the only problem of this match is that the genius 10 used around 60% of their max, which makes all the struggle seems useless.
No. 4 - Kintaro vs Dorgias
Here we have TnK in action, I like how TnK is visually portrayed and in general it was pretty, we have Kintaro dominating the match and I liked to see how Dorgias was playing here, he was keeping up with Kintaro TnK even though he was desperately trying to return Kintaro shots. But even though it was 3-3 when it became on screen it was clear that it was an one sided match when it was show how Dorgias was exausthed on the 5-3. Dorgias even having reason to slack off in the match, he was putting his life on the line and it was a really good moment when Dorgias won his fourth game making 5-4, his comeback was good but in the end he would still lose, I wanted this match to have a real end but it still enough to put on this list.
No. 3 - Shiraishi/Kimijima vs Tristan/Timothee
I need to put the most stylish match in the series here right ? I would put this here mainly because of Shiraishi, since we got his evolution and the path he choose to follow. As a fan of his Bible Tennis I didn't think I would like for him to change his style, but I liked what was done, he didn't just start to copy people like Niou and Kabaji, he used what he saw his companions doing everyday and he continued to focus on stats to overcame his opponent, the only thing that change is now he's more flashy and this match was a good place to start a more flashy style seeing who are the 4 players. Of course I also liked the france double and Kimijima surprised me in this match, by how good he were playing basicaly by himself and when he lost his "cool" appearance.
No. 2 - Byodoin vs Tokugawa
There's not much to say about this, Byodoin vs Tokugawa was the first high level match we saw on NPoT so this leave an impression. I really liked Byodoin playstyle, his world techniques and mainly the Pirate Spirit, that was cool to see (and this is also important to the first place). Personally, I have mixed feelings about Tokugawa black hole but it's alright.
No. 1 - Niou/Duke vs Bertie/Schneider
Well, this was Niou finest performance, we have Niou and Duke against 2 pros and Niou brings Byodoin into the game from the beginning, where we see Pirate Spirit in the first set and the world techniques in the second set. The third set Byodoin was already useless and I liked how Niou brought Zeus, Noah and Camus to the field (personally I tought Niou was only going to use Byodoin in this match but was gladly wrong). Even though I find Bertie pretty busted, I like him (can't say the same about Schneider) and his playstyle. Here we also saw Camus playstyle that looked pretty interesting and then we have Duke and "Camus" Howling that was unexpected for me but also taken gladly. Then the highlight of the match was in the Match point with Niou playing as himself and with Duke help getting the last point.
