Classic / Original Sets: I like all of the classic sets from Base Set to Team Rocket. Why? Well, because they are the original. I love the classic card design and it was the start of the tcg. How could you not like it? Although I don't think I have a particular favorite from the classic sets
Neo Sets: Pretty much the same card designs as classic sets, but it introduced the 2nd gen. of pokemon, (johto). Not a huge fan of the neo-expansion series, but I don't dislike them either.
E-Card sets: I don't like the design of the E-cards., the way they have the weird borders and everything. However, these sets introduced some big and much-needed changes to the TCG game, and I must admit, there are some bad-ass looking E-cards. Aquapolis is my favorite expansion from the E cards because it is awesome and is a pretty large expansion.
EX Series: The EX expansions are my favorite of all time. I grew up buying these cards, and when it comes to card design, I prefer this set. When it comes to the way they made the cards, I prefer this series. When it comes to awesome pokemon, I prefer this expansion. I love almost ALL of the EX expansions, though my favorites are probably: Sandstorm, Dragon Frontiers, Legend Maker, and Holon Phantoms. I also LOVE the Team Rocket Returns expansion, I though it was a great idea and they pulled off some bad ass pokemon cards. Not to mention the debut of EX pokemon is history all on itself. I also really like delta species pokemon, even though it was kind of a silly idea
D&P Series: I really like the Diamond and Pearl expansion series. Not as much as the EX set, but not far behind. This series is when they took pokemon cards to the next level, and we started seeing a lot more powerful pokemon cards with a lot less energy requirements to attack with. We also noticed a difference in art style and card design. I do not care for the card design as much as EX or Classic, but it is still nice. Also, many cards in the D&P series were illustrated by Kouki Saitou and Masakazu Fukuda, the two greatest pokemon card artists of all time. (Other than Kagemaru Himeno and Ken Sugimori, of course
) My favorite expansion from D&P is probably a tie between Stormfront and Platinum. Love those ones.
HGSS set: My least favorite expansion series in the tcg game. I hate the card designs. I hate the whole "legend" concept. Not a fan of prime pokemon. I hate a LOT of the art style and pokemon illustrations. And most of the cards were very bland and un-creative in the attack and effect department. I can only be thankful this series only lasted 4/5 expansion sets.
B&W series: I don't really like any of the newer pokemon cards. Ever since HGSS, pokemon tcg has kind of fallen apart for me. Although, I do prefer this set over HGSS any day of the week. But it is just plain stupid how powerful pokemon cards are becoming. It is becoming the norm for all EX pokemon to have 170-180 HP, there is a bidoof card that has 70hp and does 60 base damage (WTF?!). I just don't really like how the TCG game is evolving. The card designs are OK I guess, but I'm still not a big fan. If I HAD to pick my preferred expansion from b&W though, I would probably go with Dragons Exalted. My least favorite expansions are the plasma ones. I cannot stand plasma pokemon cards. IDRK why though, lol
X&Y: Don't really have much to say about this set. It appears to be identical to the black and white sets. Then again, we're only 1 or 2 expansions into X and Y, so we'll see what happens