Don't use auto-merge; use manual merging ands always merge the best unit. A tip - you can use for merging a full force unit. So take your nest unit and merge it with your lesser units BUT do not use the stronger unit entirely. Leave it with as little soldiers as possible and retrain it. Repeat untill you whole army is fully staffed. In this way all the units will benefit after each battle and quickly all the units will reach the status of the best unit. After several battles you will have a full uber-stack.
This is a really huge exploit. Using the best unit to merge is a legal move, but the exploit is created from retraining the spent units to full experience.
Actually from this retraining even without merging - just from retraining I had a uber-stack from hospitaliers. They were all gold and were instoppable. The number of battles they win per turn was limited only by their moving distance...
Boring.