Project Phoenix is my third-most favorite TRO in my whole collection, only slightly behind TRO-3050 Original (with the Unseen), and actually quite a distance behind 3057 (what can I say, I love space ships).
OP, love the top-to-bottom analysis of the IS designs. Don't fully agree with all your points, but do agree with most.
IMHO the stinger and wasp are a bit of a let-down functionally (visually stunning). I don't like rocket pods, but I did find that the Stinger miniature can be "fixed" by puttying up the launchers in the chest, then sanded flat, and it makes a real sweet chestpiece. Take the weight to improve the main gun or electronics, and you have a much better light scout. As a complete rebuild I put in FF and Endo, upped the ERMLas to a MPlas, and tossed a C3Slave and Targeting Comp , keeping the non-XL engine and costing only 1pt of armor over the 5R model. For a 20T featherlight, it works awesomely as an assassin and a scout.
Don't underestimate the targeting computer in the Valkyrie. The whole point of the design is to stay away from the enemy and pepper them with missiles, but if something is fast enough to get in close, that TC lets you knee-cap the bastard real nice.
The Ostscout is not my favorite Mech, but I do have to say it is the best case of "improving" both the original artwork and the core functionality of the design. All the Ost Mechs were bloody hideous things (or at least I always thought so), and now at least the 'Scout and 'Roc are pretty decent looking, and the 'Scout in particular is one of the best scouts money can buy.
Lastly, the Thunderbolt... Yeah, I'm with you, that LGauss is rather lame. I always swap it out for an ERPPC, like any self-respecting Thunderbolt is supposed to have.