Both are equally great, it really depends on what you are looking for.
While both are massive games elder scrolls is just that much MORE massive.
-Elder Scrolls will keep you busy for years, while Fallout will only keep you busy for months.
Both games are very immersive, there is a lot of lore in both games and it is really in depth and interesting, but the edge goes to fallout.
-Skyrim+Oblivion characters are not very memorable, while in fallout i still remember characters like Moira Brown or MR House. also interesting companions in fallout, (Skyrim can get really lonely with all the one-word followers).
I found that while playing Skyrim i get the feeling of "Holy shit, I am cool" but when i play fallout i get a feeling of "Holy shit this is cool!" interpret that how you want
In elder scrolls the world is familiar, the setting appeals to many a fantasy nerd, but fallout is in a very flexible setting, if you encounter something strange in fallout you can just say "because radiation!!!" but that literally means ANYTHING can happen.
Comparing combat in fallout NV to Skyrim, I can say combat in skyrim is a lot more fun then NV.
-fallout`s combat revolves around shooting (but that can be done many different ways)with other people shooting back, while Skyrim has a much more flexible combat (mainly because of spells, oh and dragons.) Not to mention Skyrims combat can be infuriatingly difficult sometimes.
The quests especially in Fallout 3 are a lot more involving, then any quest iv found in the Elder Scrolls games.
Finally, just one last thing, I find that DLC in the fallout games are a lot more interesting, including things like rummaging through an alien spaceship, exploring super-labs, or giant mutated swamps...you can't really find that kind of, uniqueness in the elder scrolls games DLC.
(to be clear i have only played fallout 3 and fallout New Vegas (plus dlc) and only Oblivion and Skyrim (plus some dlc)