Does anyone else feel like the way Lonesome Road registers what faction you're with was very poorly implemented? I'm trying it for the first time and Uylsses is talking to me like I'm allied with Mr. House - yet House is dead, I killed him. It seems like a bit of a design flaw as now most of the conversations I have with Ulysses have absolutely no bearing on my character, which is quite disappointing. He doesn't even acknowledge the fact that House is no longer amongst the living.

I've heard that what faction Lonesome Road (as in Ulysses and duster determination) thinks you are is determined by reputation and out of the NCR, the Legion and the Strip - but as far as I'm concerned good Strip reputation ≠ in love with House; I'm doing an Independant playthrough so it makes perfect sense for me to buddy-up if I'm going to have to involve myself with them in the very near future. Maybe it's due to the fact that a Mr. House quest was my first "end game" quest (I wanted to get the securitrons upgraded as soon as possible) - but since then I've done a few NCR end game quests and by far the most for Yes Man; if what quests you've done do have any effect you'd think it'd be better to have which faction you done the most for (or got the furthest with) rather than who you got the ball rolling with.

Does this annoy anyone else or am I alone with my dissatisfaction?

Their original intent with Ulysses was that he reinforced the importance of the reputation system. This was a plan even before he was cut.

Having said that, I think the only poorly managed one is....depending on how you view it, Indy or House.
Indy is only recognized if you're the type of revolutionary that blows things up, House is sometimes failed to be treated as gone when he actually is.

In some cases, like him saying NCR when you support Indy, it sorta makes sense because even though you have Indy on your mind, you've obviously supported the NCR as well on the side, and that's the nation Ulysses knows you for. The real underlying issue is that Indy fails to register properly for almost everyone EXCEPT those who ticked off the Strip, NCR and Legion.

Hmmm maybe I'll enjoy it more whenI play as Legion or NCR then, it's just unfortunate that this is my first playthrough as it does sour the experience a bit. As another minor quibble - is it just me or does the pip boy become too dimly lit to read at night in LR? I've tried using different pip boy display colour but it seems no good, even turning up in game and tv brightness doesn't seem to help a great deal.

Simple.

This is how it works.

NCR>Legion>House>Independence.

If you are idolized with the first three, you're going to get the NCR dialogue, always, because it comes first. (The Great Bear Duster)

If you're not idolized with NCR, but Idolized with at least the Legion, or both Legion and the Strip, you're going to get Legion, always, because it comes second. (A Fighting Chance Duster)

If you're only idolized with the Strip out of the three, you're going to get the House dialogue. (Old World Justice Duster)

If your reputation is "Wild Child" or lower with all three of those factions, you get the Indy dialogue. (Blackjack Duster)

The way it works is sort of silly, yes. If you're on PC, download this: http://newvegas.nexusmods.com/mods/44042

Makes dialogue and duster dependent on quest status instead of reputation.