I've said that it would be interesting for one of the big clothing manufacturer's to make a coordinated clothing system. I've been asking the same questions about optimal clothing selections for UL hiking. Personal preference and comfort levels, climate, weight and cost are the variables I have come to. Take your pick on order.
Here's my quick and dirty take on the options I have seen:
Base layer: wicking polyester or merino wool tees and briefs. Go to long sleeves and long johns in cooler weather. Many brands on this level.
Mid layer: needs definition. IMHO, that is something like a heavier base layer, like Power Stretch, heavier Capilene grades or 100w fleece. I'm out of touch on the the thicker wool options. Tops and bottoms available.
Insulation: wide range of stuff here. 200w fleece, MontBell Thermawrap, Patagonia Nano Puff. There are similar thin down garments, with MontBell being very popular.
Next step up on insulation would be thicker polyfil models like Mountain Hardwear Compressor, BPL Cocoon, Patagonia Micro Puff and others. On the down side (my pun), down sweaters like the ones made by Eddie Bauer/First Ascent, Patagonia and others.
Basic outer layers: button down nylon shirts like Ex Officio, REI, and others. Nylon pants convertible at your preference, and shorts. I'm just experimenting with soft shell pants. Soft shell jackets seem to fall off the UL wagon.
Windshirts: simple shells from 2+ ounces on up. Pertex is popular. Montane, Patagonia, Integral Designs, MontBell, GoLite, and Marmot are all players, among others.
Wind pants: much like windshirts. IMHO, only if you are wearing light shorts and need long pants coverage. I go the convertible pants route and pass on this option.
Rain shells: coated single layer shells like Event, Marmot Precip, Patagonia Rain Shadow. Heavier, tougher options like 2.5 layer Gore-Tex and others. Bi-laminates like Driducks. Ventilation is a very good thing.
Rain ponchos: some double as shelters. Mostly silicone-coated nylon (silnylon), some Cuben fiber is out there too.
So, polyester or wool for base layers and synthetic fill or down for insulation. No small amount of debate available.
How you layer it up depends on the climate and temperature range. For a thru-hike you might change seasons, climate, and altitude, so there may not be one static kit to do it all. What you can tolerate for heat and cold is a factor too.
My basic 3-season kit for Western Cascades:
Merino wool socks
Light wicking polyester briefs
Capilene silk weight tee
Capilene silk weight long johns (shoulder seasons)
Convertible nylon pants (or soft shell)
Power Stretch or 100w fleece long sleeve zip top
Light polyester fill jacket
Patagonia Rain Shadow rain shell (left out when using poncho shelter)
GoLite Reed rain pants
Tilley LT3 hat
Outdoor Research Peruvian Windblock fleece cap
Mountain Hardwear Tempest gloves (shell with micro fleece)
I can juggle a little for full summer stuff, wearing a button-down shirt and shorts, leave out a layer, etc. Colder shoulder seasons may find me in heavier pants, thicker base layers, heavier insulation. My bias is to wet weather and moderate temperatures.
The real core to an UL clothing kit is not duplicating and a selection of layers that work together in several combinations, and multiple use if possible (like poncho and shelter). In a perfect world, you should be able to wear it all in the most extreme conditions. There are two worlds you live in: hiking with a load and sitting still. The trick is to be comfortable in both with whatever Mommy Nature throws your way.
There will be many opinions :)