I have them both as well, and it depends how I feel at the time as to which one I use...I like both as well, but Trainz always seemed to run better on any of my previous machines.
I am going to give Trainz 2009 World Builder a try. Will let you all know what I think, post up some screen shots etc.
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I love Trainz. TRS 2006 to be exact. The user-friendly route making is great, MSTS is okay, but Rail Simulator is a little harder to build with.
Joshua
EDIT: As for TS2009, it does have a capadiblity mode that allows most TRS2006 content to be used, but since it's so new, not many content builders have created content. The added meshes and textures don't help with the timely process of using Blender, GMax, or 3DMax. The detail, is amazing, look at their website for comparing screenshots. SPORBUST makes great content for TRS2006 too, I'm not sure if it's TS2009 safe, but if it's in capadiblity mode, probably.
Still, I'm looking for that missing KUID for his ES44ACs.
You get what you pay for, Trainz is more expensive but it is still being made
(cant wait till for Trainz X, its got multiplayer!)
Trainz is very high quality but it is demanding on graphics, it is more easy to add content (as of June 2009, 100,000 things to download!) yet it is also eaiser to crash.
MS train sim is too simple with not enough flexibilty, in every way except on reliabilty of game, Trainz is clearly superior. The birth of modern Trainz,
Trainz 1.3(made in 2001), is better than the last version of MS train sim.