^mike,
Some good ideas, especially for someone who doesn't live here
The Cermak Blue Line's days are probably numbered, it was only kept as a political favor anyway. Either it's frequency will be increased or it will be eliminated, but you're right that the current arrangement is pretty odd.
Regarding your elimination/shortening of bus routes, this is a tricky one on a case-by-case basis. At most, some of these could be shortened during
off-peak hours only. During rush hour, the Red, Brown, and Blue lines are already so ridiculously packed that the buses are necessary just to have capacity to get everyone downtown (and even several of those routes, particularly the 22 and 56, are already packed to the gills on ~3-minute headways), so eliminating that would be a bad idea. Perhaps there could be some scaling back if the Red line ever gets a 10-car capacity expansion, but otherwise...
In some cases (I'm thinking the 56 and 21 particularly from your list), the parallel routes also serve an important function in providing local service along busy commercial streets where tip lengths are often pretty short, and the rapid transit is used more for longer trips either as a result of station location or wide station spacing. In contrast, the 62 which parallels the Orange Line functions as a feeder/distributor service to the Orange Line, which has widely spaced stations, so even though its parallel its complimentary, not competitive. The 3 is tricky; south of 63rd it is a vital neighborhood route, as it is north of about 35th street. The route is already split into several segments, with certain scheduled trips only running part of the route. I suppose the route could be split altogether, but there are some people who need to make that long trip and its probably more trouble than its worth. The 8, while running parallel to Red/Brown on the northside, provides a valuable connection for Lakeview/Lincoln Park residents to travel directly to the West Loop/UIC area without having to travel into the Loop. I would generally agree with you on the #7, and would toss in the 38 (served by Pink), X20 (served by the green line), 17 (served by pace), 129 (basic route is already served by the 1), 143 (served by 151) as other duplicative routes to eliminate.
re: closing Dan Ryan stations, it's unlikely since Federal money was just used to renovate those stations. Furthermore, the Red line is already FAST: I've timed it at under 25 minutes from 95th street to Jackson, so travel time isn't really an impediment to ridership on the branch (if anything, the route needs high overall accessibility, e.g. park n ride lots and TOD).
The clubber service may not be fully necessary; right now, the Brown Line shuttle (Kimball-Belmont) and Purple (Linden-Howard) operate until about 230am, by all means I'd just make those run 24 hours like they did until the mid-1990s. Otherwise, the other lines that don't run overnight are run by buses on 30-minute or less headways (the #62 for the Orange, 60 for Pink, 20 for Green). And honestly, this is a major cab city (highest medallioned taxis per capita in the US....yes more than NYC), which is the standard form of transport for all but the youngest and brokest college student nightcrawlers. Getting cabs at night is so easy that it's hard for transit to compete, particularly when a group of 2-4 can just pool together and spend barely more than a transit fare.