1) I'll agree with Swadian on designs insofar as if you angle your operation to fit with Googie, Googie (even if more subdued) has a place. Personally, I'm partial to the Greek/Roman-based designs of the early 20th Century, but I find "subdued Googie" (that is, toning down some of the lights and colors but keeping the shapes) to be a bit more tasteful than the wavy roofs and all-glass structures of today.
2) As to avoiding driving into DC...again, in general I would agree, but if you're really looking to drive up longer-distance train travel you need to allow for a concession on this point and accommodate long-term parking somewhere. Now, you can do that at ALX or at some of the Metro stops, but I've generally gotten the feeling that at least with the Metro this is somewhat discouraged because of commuter demand. And VRE is annoyingly unidirectional (north in the morning, south in the evening). So if you've got to park people somewhere and the WMATA isn't "on the ball", it'll probably end up having to be Union Station unless you're trying to "force" people to add a connection. Moreover, the simple presence of available parking does seem to be a necessity if you're building the station up as a major center of retail, residences, and whatnot. The trend may be towards fewer cars and it is good to encourage that, but you're still going to have tourists and the like. And then there's the Capitol, as noted...which could almost assuredly use some additional capacity. Hey, if Amtrak can make a few million off of lobbyists parking at Union Station, why shouldn't they?
3) I think that a larger portion of the reason for trains not running through at NYP than you suspect has to do with the sheer turnover volume there: NYP has just under 9m passengers per year as of FY11, while the total ridership of all trains touching NYP in some form is 17.13m, giving a ratio of about 52.5%. If there were more through traffic (and the proportion of that does seem to be rising), there would likely be more trains. By the way, I'm including the six LD trains that use NYP in this count; excluding them, I think the share may rise to 55% or so. The same goes for the "Virginia Regionals" watering down that share, as the majority of the VA business stops short at WAS, PHL, etc., or even stays in-state.
Anecdotally, the Acela basically dumps out there, even when running through. The Regionals aren't quite as "vigorous" in this regard, but even there I've gathered that NYP is a major on/off market.
4) Another point to be had here: Though it is a longer-term batch of plans, I know that VA wants to get up to 9/day to Hampton Roads, and the plans do seem to be in the works to add at least another train to the Lynchburg route (assuming that growth resumes in some form). If SEHSR plays out in any meaningful form, that's going to be at /least/ worth a second Carolinian, and probably a third eventually. The point here is that in the longer term, there's likely to be a good deal more through traffic to the south...
...and of course, all of this ignores the MARC/VRE discussions on both running trains through (to reduce on-site storage, if nothing else) and VRE wanting to add capacity and/or trains (likely necessary if the network expands by a few stops, as does seem likely over the next decade). Basically, I don't see a massive increase in trains from the south terminating at WAS, but I do see room for Amtrak to consider it wise to add platforms to accommodate a lot more through traffic over the next 15-20 years.