What kind of rewards were you getting? Also, can you elaborate more on leveling the Cryptarch efficiently?
Cryptarch starts at level 0
Every engram you buy or let him decipher nets you +50 (Common Engrams) which you can buy off him very cheap, or +100 (Green Engrams) from drops from Strike missions or enemies that you kill that drop them, those deciphered engrams add points to his Rank which you level up, you can see your rank in that circle that next to him which fills up little by little
The reason you want to level him up is the better Rank he is, the better he can decipher the lower tiered color items, but also lets you acscess to the higher tiered color engrams
You can have a Rank 1 Cryptarch decipher your blue engram, but most likely it'll net you a blue material
Say of your Cryptarch is level 12, now he deciphers it and you most likely will get a weapon/gear piece of same color or 1 tier below, the more you rank him up, the he will identify, decipher, and net you good reward
Raising his levels is not easy.
(Don't hold me to the numbers they might be off if changed for retail)
You need 2000 points to get him to Rank 1, then +100 added for each rank, so Rank 5 you'll need 2500 points
Common (white) give you +50 which you can buy off him for 250 glimmer per, they are always present, Uncommon (green) give you +100 which you also can buy after hitting a certain rank but sometime do go away they are pricier from 450-600 Glimmer Per, they come on sale from time to time
I'm guessing Rare (blue) and Purple (Legendary) will get a +150/200 in the deciphering points department
Once you start raising his ranks, every time you reach a new rank, you get a reward sent to you in the mail for getting him to that rank
I burned my rewards to see what I got and most of my blues/purple engrams turned into materials, but once I hit Rank 10, and got another blue reward, it turned into a rocket launcher, level 10, nice stuff to upgrade
So the best option is to save those rewards for down the line when your cryptarch is more ranked up and can really identify/decipher it for you
Hell the best thing about him is you save up some engrams and level yourself up in the process, the engrams have to at least match you in your level
So if your level 3 and get a green engram, it would better to save it till you are level 10 and rank 5+ with cryptarch so that engram can become something awesome
The way I efficiently ranked him up was by Glimmer farming in Rocket Yard and opening chests running in a loop around the area, running room to room where chest spawns, just kept doing the grind for 5 hours, which netted me 25,000 Glimmer which was the cap for the BETA (so roughly 5,000 Glimmer/hour)
Then I would go buy Cryptarch out, and start him deciphering stuff, then I would dismantle said weapon/gear and repeat the process till I have no more glimmer amount to buy from him
Repeat again
Once I got to 5+, he started offering Green Engrams on occasions before his refresh stock time
So once again I bought out the green version hoping to get good weapons but also net me Rank+ on him
Once I hit Rank 10 with him, I tried to see what my Green Engrams would be, and started becoming level 9-10 items (Beta cap was 8), with the rare occasion it netting me a Blue weapon in the process