Don't combine runes, just buy them from the store with IP.
The combiner is completely random, and, therefore, useless. Only use it if you have a ton of runes you DON'T WANT anymore or want to clean up your runes page, but that's rare so long as you don't waste your IP.
Personally I think they should remove some of the ****pier runes from the game or base the upgrade as a % chance based on which runes you put in. (So if you put in 3 crit chance runes and 2 HP runes, you have a 3/5 chance of getting Crit Chance and 2/5 of HP, rather than 100% random)