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If you care about resale get the newer one. If you care about simplicity the EJ25 is probably the way to go, just fewer "large" issues and the head gaskets are well known and not that difficult to deal with like oil consumption. I'd R&R all the timing gear though at 15 years old. All new Subaru pulleys, belt, and tensioner. Or at a minimum the belt and lower cogged idler (by a long shot the most likely to fail)

I don't know if there's a definitive procedure for creaking bolts. I could tell the if a creaking bolt has gone beyond it's yield, it just feels springy when you tighten. A good bolt can creak too, it's sometimes due to the threads in the block not matching the threads on the bolt. Good bolts that creak still feel as stiff as ones the didnt creak. I run them in and out a couple times lightly with a drill and clean/relube the threads. then try again. Be aware MLS gaskets deform as part of sealing, and then bite a bit into the aluminum at final torque. You shouldn't loosen the bolts all the way once you started, if you need to work on a problem bolt, back off the other bolts as little as you need to and always leave them in tension. At the torque wrench stage, try and keep everything creak free. Keep cleaning and relubing if needed. After that is the 1st 90 degree stage, some likely creak, you need to remember the feel of the good bolts and decide. It's the last chance to back off and redo. The second and final 90 deg stage, if it's a bad bolt you will definitely feel it. Never go more than 180deg total for those two stages, if it felt loose after the two stages... it's overstretched already.