I have been training in Hapkido for around 2 years, and I have just switched to Aikido a few weeks ago. Not necessarily because Hapkido is worse or Aikido is better; rather, I was driving farther to learn Hapkido at a dojo that placed more emphasis on their Tae Kwon Do class... When I started, Hapkido class sizes were 4 to 6 individuals. For the last year, it's been myself, another mid-ranked student, and an instructor. I left to find a dojo, be it Aikido or Hapkido, that focused solely on one of those arts, and I found that in an Aikido dojo.
Cross training in Hapkido might be something you would say "oh that's a different way of doing it", but in my experience, depending on how you are being taught Aikido or Hapkido, they may contradict. For instance, in Hapkido I was taught to tense up my wrist, extend my fingers to "let my ki flow" while doing the moves. First day in Aikido I was told that rule #1 is to stay relaxed at all times. That will be a hard habit to break.
Also, I noticed some of the techniques I was being taught in Hapkido were changed somewhere along the line in Aikido. For instance, this video of Nishio Sensei explaining a bad way of doing Shihonage was how I was being taught in Hapkido (Ba Gat Hye Jun was the Korean name) http://www.youtube.com/watch?v=o9PTM...eature=related
Some Hapkido instructors focus more on the aikido-style techniques, while others have fully fused in the kicking/striking from Tae Kwon Do. I have found quite a bit of variability associated with dojos (at least here in the east coast USA - Connecticut area) who claim to teach Hapkido.
So, just my 2 cents from my experience, I would stick with the Aikido and find a different art to cross train with. Certainly you can learn and take something from any art, but I would pick something other than Hapkido with an Aikido background.