From what I remember a combination of a lot of factors, some that had started previously. We had a terrible run-in in the league after the league cup win iirc.
Some factors I think contributed:
-Ramos was pretty extreme on fitness and health. The "took away the ketchup" stories seem petty, but I think it illustrates the situation. I think we had a lot of players that just weren't up for, used to or motivated for that kind of dedication as footballers. As a result I think the players didn't respond 100% to his instructions and this contributed to his downfall.
-Our transfer dealings. I think Berbatov covered up a lot of faults during his time with us, he was extreme. Midfield passing didn't work? Hoof it to Berba and he could make it stick. Goals from nowhere, assists from nowhere and so on. I think this was true both for Ramos and Jol btw. In addition Berbatov and Keane was a very good strike partnership. We essentially replaced that with clearly inferior players that in addition couldn't form a partnership for the life of them. Not only did we no longer have the magic, we no longer had a functioning attacking force.
-Other imbalances in our squad. Primarily the lack of a defensive midfielder, something we'd struggled with since Carrick left. Zokora was no replacement. Again I think the majestic awesomeness that was Ledley King covered for this to some extent at times previously. But it was a glaring problem in our squad and one our manager and DoF failed to rectify.
-I'm not sure Ramos ever managed to find a team that worked in that 2 from 8 season. He was chopping and changing from game to game. Probably as a result of the previous factors I mentioned, but he just couldn't find something that worked, at all.
I agree with you that he looked promising, the league cup win was obviously a huge positive. I also think that some of the ideas he tried to implement, like higher fitness levels and better nutrition were good ideas. He just didn't find the right way to implement them, or the right players to work with perhaps. In a different universe, where it didn't all implode as spectacularly, perhaps it would have worked over time. I always thought that he was influential in making Tom Huddlestone the player he became by slimming him down and making him a bit more mobile for example.