this is a really good question, and I'd like to give you a response to that might sound a little crazy. i'm a college coach, and we run a tremendously hilly course each year that is really important to our team. we don't have the luxury of doing repeats (short or long) using hills, and the hill training we have is mainly running up the side of a mountain for long runs, and back down for the 2nd half.
I tried something new this year, and the results blew me away. we did short hill sprints (maybe 160-180m at the longest) a few times this season in the september and early october. we alternated short-long (90m/ 180m) for a total of 12-16 repeats once, but i really like using hills during sessions like mile repeats, and it's not an option. the biggest change came in the form of hurdle drills. we did 5 drills that focused on increasing the flexibility of the hips, and increasing the knee drive--which is essentially what one needs to become a better hill runner. I was astonished with the results--we ran hills on this course better than ever before. the athletes would crest the hills and pass people with tremendous strength and ease, and our results were the best they'd been in years. in fact, most of the juniors and seniors said that this course seemed easier than it had in the past--but the course hasn't changed in 20+ years!
since you're asking for advice, i'll tell you what we've done to increase our success with hilly courses:
long runs fall into one of 3 categories:
A) 20-22% long run: (meaning 20-22% of our weekly mileage. keep it longer and at an easy pace on a easy course)
B) Progression LR: 90 minute long run with the last 2-3 miles run at threshold pace--go by feel. most athletes would run the last 2M at 8k race pace.
C) Standard LR: 18-20% long run on a challenging course.
Hurdle drills. I searched youtube and spoke with other coaches about what to do, and how to do it. it's not hard--just walk over hurdles, make it fun and do the over-under drills. there's a good vid on flotrack that shows the AZ women's team doing hurdle drills and we do something very similar. you may need to pay for it--i don't remember.
good luck!