With a bit of work, you can make a system based off transmutation
Incantations. (seems I've been linking to this section of the SRD a lot lately)
Since you don't want magic items to be too common, change the "casting time" from every 10 minutes to every day (so at minimum it takes 6 days) and the extra long check every hour to check every week.
Unlike the Incantations presented in the SRD, these aren't rituals per se, instead, it's a guideline for how long it takes for you to get the benefit of your ordeal.
Example
giving a +1 weapon the Frost ability
Transmutation base DC 34 +22 for Instant duration, -4 for touch range; target: 1 object of up to 20 cu ft. Saving throw Fort (harmless) Spell resistance: Yes
Currently that's a painful 52 DC
Skill checks we'll make the checks required the appropriate craft and Survival (for a total -2 DC)
Limited Target (weapons): -3 DC
Expensive Material component: difference between a +1 weapon and a +2 weapon is 6,000 gold, or 3,000 to create. We'll bump it up to 5,000 gp since you want it rare anyway ... -2 DC
XP Component: 5000/25 = 200 xp so -2 DC
Backlash: Caster is exhausted: -2 DC
Failure: 5d6 cold damage to caster
So from 52 DC to 52-2-3-2-2-2= still a daunting 41 DC increasing the material costs, XP cost or adding some hefty backlash can take it down further (if you lose 1,000 xp, instead of 200, the DC drops to 33) ... then because this is a 6th level effect (the minimum), you need 6 successes (1 day between checks, doesn't fail unless you fail twice consecutively)
Just a thought