I've played and run both BRP and d20 CoC and the more I ran the d20 version and used the manual, the more I realized that I prefer the BRP version.
For one thing, I like starting investigators as highly competent professionals, very capable in their fields. With d20's level system and everything tied and advancing together, it's not as satisfying as being able to spend my points in my educational fields in BRP.
The magic system, I think, works better in BRP with its magic points, POW scores, and so on. Powerful cultist sorcerers are more fun to play as a DM in BRP than in d20 because they aren't always eating their STR or other stats to cast spells.
The Cthulhu mythos skill and issues surrounding it, especially sanity effects, work more seamlesslly in BRP as far as I'm concerned.
I'm also not too keen on the d20 manual's organization or presentation of some of the rules. The firearms section is particularly vexing to me.
Now, d20 CoC isn't a bad game. Not a bit. I just don't think it's as good as BRP.
And, by the way, there are TONS of materials out there for BRP, if you're willing to chase down out of print materials. Aside from Horror on the Orient Express, most adventures I've played in aren't particularly linear and I've played in many.