I don't think it is a mistake to play things over the long term and let on that there is something building, lots of things do that and it is fine. Where I think he ran into problems was that he lost forward momentum on the Malekith front, and more specifically what exactly Loki, Thor, and a couple others are doing in that whole situation, for a large chunk of the time Jane was around. What I suspect happened is that Jane was not supposed to last nearly as long as she did, but she was more popular than anticipated, and other writers wanted to use her on the Avengers and stuff, so Aaron padded out her story to allow that to happen. As far as Jane specifically went, it worked ok, but the War of the Realms plot slowed to a crawl in the background because I presume he wanted Thor Odinson to be the one with the hammer when it wrapped up. If it had kept momentum going, and wrapped up when it was probably originally planned, it would have been fine. But it got stretched out so it feels like Malekith and Loki and a few others spend a lot of time just sitting around. I mean yeah, we'd get reminded of it from time to time. Fairly frequently we got at least a little tidbit of the whole War of the Realms thing, it wasn't dropped completely or anything, but it was moving forward at a snails pace, which resulted in Malekith etc. not actually accomplishing much, so it didn't feel like as much of a major threat so much as sort of a background annoyance
*edit - I have decided to go with markers... but not JUST markers. I ordered some metallic gold paint and I think it might be neat to use that on all his shiny gold costume bits. (along with the blackest black paint you can get, which i may use on the hair. we'll see.) But the rest, I am still deciding on black and white (the markers i ordered are all grays) or colour. if colour, i will need to get a couple colours, (I am re-building my marker collection, i have a few holes to plug, most notably in this case, I need a yellowish green and some flesh tones) which may take a while.