Lois and Clark do end up together, and though there's been many clues (or "anvils") that they will, DC said that the one condition of Lois being on Smallville was that she and Clark were not to get together on the show. So, in a way you are right when you say that Lana and Clark will end up together on Smallville, because they probably will. On Smallville. But eventually, he'll move on to Lois and she'll move on to Pete and we'll get Lois & Clark, even if we never get to see them together in their current incarnation.
Even if that weren't true, Clark can't stay with Lana. She's holding him back and preventing him from accepting his destiny as Superman. He spent almost the entire 6th season in his barn moping over Lana when he could have focused his attentions elsewhere. Instead of almost Superman Clark, we got a Clark that let Oliver and Chloe do all his work for him. Lois is right for him because she would never hold him back. (Personally, I'd rather see him with Lex or Chloe, but that's just me.)
(It's actually season 4 that Lois came on the show. :) )