I agree with Jim; mods do absolutely nothing for resale value or trading. Over the last 10 years, I tend to buy higher end instruments and if I mod them, keep the original parts. They are more valuable this way when reselling or trading.
As far as Fenders go, I still feel the best bang for the buck is a used MIA. There have been some very good deals out there in the last couple of years if you watch the used market and know your stuff.
I have owned 3 Fender Strat's in the last 10 years, an American Deluxe, an American Standard and a MIM. I traded the Am. Deluxe for a Gibson LP about 6 years ago. Last summer I traded the 2013 American Standard for a 2013 Gibson LP Studio. I kept the MIM.
The MIM was originally purchase as a back up instrument on the used market for $220; with the sole intent to modify it into a gigging back up instrument. Pretty much everything has been modified on this MIM; infact the only original part still left with the guitar is the body itself. The neck got changed out for a new MIM neck back in August when it needed a fret job. The block was replaced with a heavy steel block. The bridge was replaced. Tuners replaced with Fender Locking tuners. The pickguard was replaced along with the pots when I bought a fully loaded pickguard and pick ups from an American made Strat off eBay. I have gone through the original pickups, the American made pick ups, Duncan Texas Antiquities and Duncan stacked pickups on this instrument until I settled into Rose Pick Ups, custom wound to a Gilmour mix of neck, middle and bridge. I will never get anything more out of this instrument than it being a used MIM Strat, but I kept it as my main player because it was so heavily modified, that it played every bit as well as the expensive Strat's that I owned; and got most of my playing time, for Strats. I used the bargaining power of the better instruments as trade for other high quality instruments.
If I was to start over again, however, I would buy a used MIA Strat and change PU's until I got it where I wanted it.