Having grown up in Iowa, this series really reminds me of the Iowa-Iowa State series. I even remember listening to Iowa fans say that playing Iowa State only helped the Cyclones and did nothing for the Hawkeyes and they should cancel the series. In fact, an Iowa fan in my office just made that exact comment to me last week when we were talking about college football.
Aside from that, if you look at that series historically there are some parallels. Iowa and Iowa State have played a total of 61 games with the first game being played in 1894. Iowa has won 41 of those games. From 1983 to 1997 Iowa won 15 straight games over the Cyclones. Similarly, CU went 9-1 against CSU during that same stretch in 10 games. Both series actually started to get competitive again around 1999 to the present.
http://en.wikipedia.org/wiki/Iowa–Iowa_State_football_rivalry
http://en.wikipedia.org/wiki/Rocky_Mountain_Showdown
I know it is not a perfect comparison given that Iowa State is in a BCS conference, but I think overall profiles of CU and CSU are very similar to Iowa and Iowa State as institutions and the fans view each other in much the same way. Iowa has never respected Iowa State and the fans hate each other for it.
Iowa State - Iowa is a very valid comparison in that Iowa has been a traditionally successfull program for a long time and ISU has not. Iowa has never reached the levels of some of their B1G conference mates like Michigan or tOSU or PSU but they have had and/or been in the running for Rose Bowls and other major bowls, been highly ranked over multiple eras etc. while ISU has had some limited success but traditionally been in the lower end of their conference and sometimes been at or near the bottom of the college football world.
There are a couple of big differences as well though. One is as you mentioned ISU is in a major conference. When they are bad it is because they are losing to Oklahoma, Okie State, Texas, etc. CSU when they are bad is losing to Wyoming, UNLV, and Utah State, much less notable programs.
The other big difference is that Iowa and Iowa State are the two significant sports enterprises in Iowa. Yes lots of people in Iowa are fans of pro sports franchises with strong interest in those located in Chicago, St. Louis, and Minneapolis but within the state Iowa and ISU are the two top dogs.
In Colorado CU isn't competing with CSU for top dog position or even close. This is first and foremost a Bronco state with the other pro franchises also drawing a huge degree of allegiance. CU is easily the top non-pro sports enterprise but they aren't competing with CSU for interest they are dealing with the pros. It could be argued that CSU isn't even next in line since the AFA draws bigger crowds, better TV numbers, and more national interest and respect.
Iowa is also a different situation since a much higher percentage of Iowans have family and cultural ties to the state. It is not close to as transient a population as Colorado. The Iowa schools are also not dealing with competing with the array of other entertainment/recreational options that CU (and CSU) have to.
The core fans of CU-CSU do dislike each other but unfortunately for both schools the majority of people don't care that much. College football simply isn't a big piece of the fabric of life like it is in many other places.
I went to CSU, did my master program there. I like the school and a lot of the people associated with the school. My personal view is that CSU is throwing money down a rat hole trying to maintain a major college football program in an environment where the powers of college football don't want them and the majority of the people who would be their supporters don't care.
This is not to say that CSU doesn't have a core of very dedicated and interested fans, they clearly do. This core has stuck with them through disappointments and lousy seasons, through conference turmoil, through repeated coaching changes, etc. Unfortunately this core is not large enough and more importantly financially viable enough to justify CSU continuing to try to enter and compete in the world of major college football.
I think that CSU would actually be much better off to build a 18-20k stadium on campus and go after success in the world of FCS football. Be a big fish in a smaller pond instead of a bait fish in a swarm of sharks.