All cards are theoretically allowed. That being said, I try to balance decks downward, and modern archetypes are more vulnerable to losing fundamental aspects of their playstyle. Of particular concern:
[list][*]Monsters that are immune to a lot of different forms of removal/destruction by battle and demand rarer/more specific forms of removal are a big issue, since I don't want to put that onus on decks.
[*]Decks with strong swarm, which can consistently keep a board filled with monsters that aren't pushovers.
[*]Decks with a lot of removal, which can consistently wipe enemy boards.
[*]Decks with a lot of negates/field/hand control, which, if allowed to setup, will go on to deny the opponent from mounting any resistance[/list]
None of these are a problem by themselves, (except maybe the first one, if they end up immune to all monster, spell and trap effects + too difficult to destroy by battle) though in conjunction with each other they make it difficult for decks built around bad cards and archetypes to compete. I'll usually ask for something to be removed, which is generally not a hard and fast ban, but may come with subjectively unacceptable caveats. Older archetypes (especially those who have been around for a bit and thus have slightly worse cards to fall back on) are usually easier to balance and don't need as much hard and fast limitations.