I actually used to play a little modified back in the ruby and sapphire days and stopped around fire red and leaf green or team rocket returns. I don't remember which came last. This was quite a while ago, but I'll see what I can remember. Ruby and sapphire was modified while expedition, aquapolis and skyridge were also modified and oracle with energy draw delcatty was very common (in my area at least). fire starter blaziken was also a popular card in my area and it was used with team aqua's manectric quite often to keep a steady supply of energy to the active pokemon. A lot of decks were also evolution decks thanks to rare candy getting printed in sandstorm and kind of became a staple in many decks. ATM rock was also a card used quite often to cripple these rare candy evolution decks and steven's advice was in nearly every deck in my area. The only thing I really remember after the rotation of the expedition block was dragtrode since I started to play less during this time. This deck used dark electrode to get your dark energy out of the deck very fast and dark dragonite took the energy off with its dark trance poke-power. Rocket's sneasel was usually the deck's main attacker and could hit for a little over 100 early in the game and 100 was enough to OHKO most non-ex pokemon. A lot of ex pokemon were honestly very risky to use since nearly all supports didn't help them in any way, and only some decks would actually use them. I also noticed how many players seem to love the card N, and this era has the same card named rocket's admin. Rocket's admin was also a great card, but I'm sure most people know this from playing N.
Maybe some others can give better information, but this is what I remember in my area when I played. I also remember that deck building used to be a lot of fun and the cards let you get very creative. Decks didn't rely on ex pokemon too much and they were nearly all evolutions. I really don't like what has happened ex pokemon and can't see myself really getting in modified.