It really is a matter of taste and personal preference. The PQ commute to UCSD is at least 10-15 minutes better then the CMR commute depending on what part of PQ you are in. I would not recommend the northeast area. Some of the pricing has crept down to the low-mid 500’s for 1600 sf types of homes down west of Black Mountain. there are some homes that are the size you want (2k sf) here but not in the low 500s. There are some larger homes north of Black mtn on the side of the hill that are not bad but are a bit more expensive. The housing stock in this area ranges from 70s to mid 80s. If you want nice 92129 which is still techincally PQ then you go west into the Torrey Highlands. You will have to pay Mello Roos for these homes and they are going to be in the 700s and up. Much newer stock though being built in the 2000 timeframe. CMR has a newer stock of housing. You have alot of stock built in the mid 80s, the 90s etc. Most of the CMR homes will have Mello roos associated with them. If you travel south you run into Sabre Springs and they to will have MR but are of the same quality (for the most part) as the CMR homes.

As far as holding values…tougher question. I think that CMR and PQ (for homes built in the same timeframe) will hold pretty much equivalent values. I would give the nod to CMR but it also will more then likely have a higher cost of living due to the MR and potential HOA fees. Both areas have pretty ample park areas, CMR has the shopping area off CMR road near the 15. PQ has the Vons down off Black Mtn. There is the Albertsons off of the 56 if you want to stretch into Torrey Highlands for PQ.

Since you are in no rush to buy why dont you try renting in one of them for a year to test drive it and see what ya think.