Hmm... Interesting questions.
2. Leon (He's noted as a prodigy, and his duels against Rebecca and Yugi easily show his skills.)
5. Pegasus (I put him above Kaiba for a probably unfair reason. Unlike Kaiba, Pegasus seems to still be a somewhat active duelist in GX, whereas Kaiba had already basically retired by the near end of the original series. He also lacks the weakness of lot of other good duelists in the anime share; a lot of them can be very overconfident at times, and often underestimate their opponents. Pegasus only did for part of his duel against Yugi.)
...and I know this was meant to be a top 5, but I feel uneasy about the fact several people didn't make it.
6. Kaiba (He's this low because of his effective retirement as of the Grand Championship, and because of his constant underestimating of his opponents, including Yugi, Pegasus and Joey.)
7. Bandit Keith (While he does cheat, he's also a very skilled duelist, and one of the very few that clearly shows strategic choices in his decks (he used a Machine deck in Duelist Kingdom for their immunity to magical attacks, for instance). There's a reason why Bonz, Sid and Zygor followed him, and like Rebecca, he was/is a high-level tournament duelist.)
8. Mai (She's very confident, doesn't tend to underestimate most of her opponents, and like several others on this list, is a high-level tournament duelist. She's occasionally too overconfident, though, such as against Marik.)
10. ...This spot is tough.. I guess I'll give it to Marik, since his intimidation and wear-down tactics tend to be rather effective. But he overestimates his abilities, and lost to Yugi and nearly lost to Joey because of it.
Honourable mentions go to Odion, Valon, Joey, Weevil, Dartz and Siegfried.
I didn't include Atem because we honestly didn't see much of his own dueling ability, and he seems to have peaked by the beginning of the series, so he didn't improve much. He also gives into his anger a lot. (Which is how he lost to Rafael, and was very, very evident in both his duels against Weevil, particularly the Waking the Dragons one.)
Best decks is trickier... Let's go entirely by their in-universe decks, ignoring the competitive game altogether.
1. Kaiba (He has a very well-rounded deck, with one of the more aggressive monster line-ups, and a lot of good Spells/Traps.)
2. Rebecca (She *gasp* actually uses strategy in her deck. Which is honestly, sadly, pretty rare...)
3. Valon (Basically entirely because individual cards of his are very broken, particularly Full Armor Gravitation, Phoenix Gravitation and Big Bang Blow.)
4. Siegfried (See above, but it's his Goddess Spells this time. Not so much Ride of the Valkyries, despite his tendency to pull off/attempt OTKs with it.)
5. ...I'm honestly not sure who to put here... You know what? I'll actually say Seeker. His deck has flaws (as noted by Yugi), but it's also a very powerful Exodia deck. The problem is, Seeker is horribly incompetent as a duelist.
Yugi/Atem didn't make the list mostly because of their constant habit of running bad cards in addition to their good ones. (The amount of times Yugi has ditched Chain Destruction with Emergency Provisions or Card Destruction is very telling, as is the fact he still had Feral Imp in his deck in the Battle Royale to determine the pairings for the semi-finals of Battle City.) Runners up include Mai, Keith (especially after his deck was augmented by Marik), Marik and Strings.