AIkido principles works just well in the clinch. I would argue that the clinch is within the context of aikido. In fact done properly it demonstrates the concept of ikkyo quite well. Ikkyo in principle, not in form.
In principle ikkyo is about controlling the spine accessing it from the shoulder area. Clinching right and it is about irimi as well.
Watch a good MMA guy in the ring closely. Especially when the are against the cage. They will pummel, underhook, control the shoulder to the spine, irimi and spin the opponent against the cage.
Glad you mentioned the Clinch William. IT is the first thing I'd recommend that someone learn if they are serious about fighting.
You can catch punches just fine....it may just not be with your hand!
Clinching puts you in a range that negates his ability to punch and improves your ability to effectively use aiki principles.
We have to be careful not to confuse the kata that we train with to teach princples with practical application. However just because many don't train the clinch does not mean that it cannot contain aiki principles.