I see what you mean with breaking the game though, so maybe upgrades should be fairly pricey. Or, each outfit has a "weight". So say, a final outfit may have a weight of "4" which means it can handle four average stat bonuses, whereas if you engrave it with more powerful stat bonuses (say perhaps the 25% chance of stun I mentioned), that stat since it was so powerful would have a different "weight", say "3.5" so that then you could only add "0.5." of extra stat bonus, which may perhaps just be the player trying to slip in a small attack bonus. Of course this would all rely on the first example I gave ("I want to have X amount of critical chance") rather than "I want improved critical chance") ... though I suppose the latter could work.
Of course applying some border conditions woul help, using the property multipliers of the equipment would balance things further (say a chest piece can handle 10 "weight", and a helmet only 5 since this item types multiplier is 0,5 ... so simply apply DA2 scaling system)
and if you set some reasonable cost ratios for the various effects (e.g 1% crit chance costs 0,2 weight and 1% stun chance 0,4) you have a decent chance that nothing terribly broken is possible... and then you need some way get the actual item lvl in the equation, adjusting the cost ratio would probably be the easiest solution(so on a low lvl item 1% crit chance uses more weight than on a higher lvl item)
But with the addition of "weight" I think the system is even more similar to the rune concept, albeit it is more flexible (you can decide to have a lot of very small enchantments, while if you have 3 runeslots available you can pick a maximum of 3 different effects...)
The thing I liked about runes in DA:O was that the investment was not lost since you could just remove them and put them elsewhere. So you could 1) put anything in a runeslot without worrying that you could have found something better for the slot and 2) you could put a rune anywhere without worrying that the rune might be wasted in this slot (because you find better stuff shortly after) So this is a point where runes are more flexible^^ ... unless you can undo the applied effects again and get your money back...
But imo Bioware should make a few additions to runes: Apply the concept of "power lvl" to runeslots as well, so putting a rune in a slot has a greater effect than putting it in another slot ( e.g an item has to slots putting a rune in slot one grants +10% dmg and in slot two only +5% since slot one has a higher powelvl), and represent all effects with runes (so you find an item that has some runes preset that you can remove, instead of finding an item that has some "static" effects preset, rare items could have rare runes that you can still remove and put in other armor if you wish)
I like the idea but still think the overlap with runes is rather high, but still... having both systems wouldn't hurt xD