But whatever, I'm still enjoying the game, so let's see what they do with these new twists.
What you're saying is sensible and I agree with the logic there (good one on the Pale Tree in particular).
If we consider Tyria and Guild Wars 1/2 to be the only things in existence, then yes, there may be cause for concern and so on, it wouldn't make sense, we'd be tearing our hair out, and so on.
The issue is that these things do not exist in a vacuum. Guild Wars 1 was released in 2005, in a particular context. ArenaNet (itself comprised of several ex-Blizzard employees) was vying for a space in the market that was dominated by WoW and Diablo 2 (the latter still very much in its prime). They hashed together a game, albeit with very interesting (though patchwork) lore, and released it to compete with those titles, even though they claimed they did not intend to compete with WoW directly as GW1 was not strictly an MMORPG to the extent WoW was - though everyone could read between the lines and see that that's the direction ArenaNet was going in and was hungering for the MMORPG market.
Anyway, I am sure that ArenaNet knew there was no guarantee that GW1 would succeed, and so did not have initial plans to expand this. It is highly unlikely (in my opinion) that ArenaNet was looking that forward into the future when they were developing the lore for GW1. It was simply impossible both to foresee the future of GW1 and to plan for so much growth in the game series and universe. They probably did not even think of the Factions and Nightfall expansions of GW1 when GW1 was initially released.
The truth is that videogame companies work on tight schedules and rapid turnaround - they do not know what lies beyond the next hill, let alone across the valley. It is not realistic to expect 100% consistency in lore and especially across the 9 years that the Guild Wars universe has existed in.
There is a major difference between videogames and works of fantasy fiction, for example. In the latter, the authors can spend years refining and fine-tuning their universe and story (Tolkien took decades). Videogame companies do not have that luxury. They spin whatever yarn works for the next game, and let the chips fall where they may, leaving the job up to those working on the lore and story to patch together whatever makes sense for the next game, if there is a next game. So we shouldn't worry too much about these lore wrinkles. Try to close one eye, give them a break, and realize that what they've accomplished is still quite extraordinary given the constraints they have had to work with regarding the videogame industry (and don't forget the undoubted pressure from NCSoft to meet their particular criteria, such as for example banning them from exploring Cantha again and whatnot).
I, for one, don't mind (for example) that the Pale Tree is at the centre of the universe now (even though it's logically strange based on previous lore). One final thing - just because it doesn't make sense now, doesn't mean it won't make sense later, with more unfolding of the story. It might all click at one point. Who knows? And why not enjoy it in the meantime?
EDIT: the "you" implied in the last sentence is universal, speaking to all those who have expressed qualms about the lore, not to anyone in particular.