You didn't note if you're installing your mid-compact or still working with your 53/39. I assume you're running a short cage rear der (derailleur)?
Either way (standard or mid compact) the large/large method is your best choice for establishing length. ( i.e. wrap and add two links.) As noted, this protects your system if you shift into the large/large combination (cross-chaining), which isn't a good idea because of chain angle and heavy wear.
The small/small method is more of a check to determine if your der cage has enough "wrap capacity" to take up slack for extreme drop ratios. Small/small is again not a desirable combination in-use because of stress and wear on the driveline. However, new school doesn't seem to be as concerned about cross-chaining - "use all the gears you paid for and replace when things wear out".
A short cage Shimano der with 11-25 and standard or mid-compact rings should have no problem taking up slack. If it was me, I'd set it up using the large/large method, then assemble. Run through all the gears and see if you have excessive sag (or rubbing) in the small/small combination. If it does rub or have excessive slack and you plan to ride small/small, then you will want to tune out the rub in some way. You can adjust the B-screw to add some tension into the system, but that can have a negative impact on shifting response (not as quick/precise) across your cassette. Scott43's suggestion to follow Shimano protocol is a better idea if you're going to ride small/small.
If you run your chain a little "short" for the gear combos you have, you can tune the system for slightly more crisp shifting. Depending on how short, you may need to be very careful you don't shift to large/large. If the chain is too short for your large/large combo, best case is the system will bind and not turn. Worst case - something will break/bend ... most likely the rear der.
Depending on what you optimize for, you can probably swap in/out a 2-3 tooth cassette difference without resizing your chain. (i.e swap an 11-23 for an 11-25) On rare occasion I swap in a wheel with an 11-28 in place of an 11-23 without resizing my chain for a very hilly ride. I just know I cannot shift large/large - or even large/2nd large - without undesirable consequences. Driveline set up is a bit like choosing skis - what terrain are you going to ski most and optimize for that.
There's also a "calculation method" for chain length. Probably on Sheldon's site somewhere. Probably more appropriate for a high-travel mountain bike, where you need to account for many more variables than a fixed rear-triangle road bike. I'd keep life simple and use the large/large method and be done with it.
Edited by medmarkco - 4/7/14 at 1:16pm