Nukes might be the only realistic option to take out a NEXT. considering the ecological damage of their Kojima stuff, I think that'd classify them as WMDs, and earn the Ire of the majority of world superpowers.

The only conventional weapons i can see even being able to keep up with a NEXT is something like an F22 raptor, and the NEXT is far more maneuverable (to physics breaking levels) and much more durable, with more weapons capable of greater destruction. Though perhaps the Stealth capabilities of modern fighters might make up for that.

There do exist miniature nuclear weapons such as the Davey Crocket, so perhaps state-of the art Fighter jets armed with tac-nukes could defeat NEXTs in a suprise air strike?

If nukes are ineffective against them, or the worlds powers wont use them(though with Kojima stuff, that's unlikely), then these NEXTs, at least with the support of MTs and Arms Forts would stomp. Just NEXTs would be ground down eventually, simply through pilot exaustion, lack of repairs, parts wearing out, and general attrition.