[Alastor Mobius Toth]

Nukes, or for that matter most WMDs are not very effective against BETA. For one, Mankind already has lost a lot of ground, using WMDs as a part of "scorched earth" is counter-productive, as it destroys the very area you're meant to protect, plus the fallout will make it indefensible for human troops in the long run. Plus, BETAs are also pretty much immune to radiation.

S-11 is about below N2 in power, but no-one actually thought of it as a defensive weapon. My guess that placing minefields of those would be too cost-inefficient, given that most defensive lines are on the coast, or would require near-constant replacement. Plus, I'm sure that continuous usage of tactical nukes would probably blow up the defensive lines as well; whereas placing minefields more to the inlands would be both expensive (you'd have to cover a huuuuuggggeeee stretch of land), plus there's no guarantee that BETA would pass through it - you'd have to herd them via military operations and artillery fire, and the cost of losses would probably equal it with already practiced static defense actions.

Also, while it's not really showed in the anime (or for the matter, the Alternative itself), typical defensive line is composed of tanks, IFVs, Artillery, conventional mines, TSFs and helicopters.
Battles near the coast will also involve all manner of ships.

The problem is that the BETA enjoy ungodly logistical advantage, with near-limitless numbers and capacity to replace all their losses in short period of time. No amount of WMDs can fix that, since no WMD can really touch BETA hives.