can i use his ability to equip him something like an Entropy Aegis armor? (assuming i didnt team up with Team Superman)

Since his effect says equip you may only put it on a Team Superman character.

punisher's ability says:

Whenever Punisher attacks or becomes a defender, if he is unequipped, you may put an equipment card with a cost of 1 or less from your hand into play equipped to punisher.

its somewhat confusing as it says put into play, and that should avoid any recruitment restrictions, any other opinions? has this been ruled before?

The 'Equip only to ...' is not a recruitment restriction; It is an equipping restriction. You can only legally place an equipment with that kind of restriction only on that type of character. This includes putting it into play with an effect like Cyborg or Punisher, or transfering it with an effect like Mr. Fantastic or Wayne Enterprises.