For me personally, And I have played both for years now (Warhammer since 20+ and Warmahordes a good 8+), It goes to Warhammer 40k.
The reason is the overall judgment when looking at all aspect of the hobby.
First of, it has better models, and "better" in terms of both quality and quantity and also in the pure volume that GW pumps out.
It has cheaper models on a model by model basis (and I know most Warmahorde players will deal the "Buh its a skirmish game!" card). And combining this with the above, I am not pleased to pay even the same amount of money I give GW, for a model thats 15 years behind.
The game mechanics, while this is the area where Warmahordes shine, it only has one game mode that´s truly good and thats steamroller. Any other mode and youre trying to make the game in to something it is not a beer and pretzel game. And to be frank, GW does those types of games far better. So combining the new 8th edition and all the alternative gaming modes, be it competitive, open play or narrative play, you just have so much to pick and chose from it takes down warmahordes by sheer volume. There's something for everyone, and while Warmahordes competitive level of games are better than 40k competitive level of games, 40k simply offer so much more.
The fanbase. Personal experience so take this in to account. I feel that most Warmahorde players, while not evil power gaming bastards, do tend to favor the competitive gameplay. Many even view this game as the "sport" of miniature wargames, and who´s to blame them. Don't get me wrong, 40k has its fair share of powermonger´s, but these can be reasonably easy to both spot and avoid if you want to. And on a larger scale, the community as a whole is just so much bigger for the 40k game. To put it simple, you cannot go in to a miniature wargame shop, and not find a game of 40k.
I would personally pick 40k on all accounts if I had to chose.