So many good suggestions for how to choose. Another one that I can think of is to flip a coin. Heads for Kaiden, Eagle for Garrus (fitting) and see how happy you are with the results. Hopefully, that might help narrow your feelings.
Otherwise, it'd be good to list what you value in a partner and compare just as a previous poster mentioned the pros and cons between them. Kaiden has a lot of depth and is a fairly well-rounded person (if you don't turn him into a xenophobe) who will take a good long look at both sides of a debate. He takes the time to see past the initial impression and analyze the rest before he makes a decision. To sum it up, Kaiden is a thoughtful, rational person with a philosophical bent. On Horizon, he proves that he can hold to his own beliefs even against people he respects highly. Downside, I wanted to punch him for having a snit fit and jumping to conclusions about Shepard willingly betraying him without considering that she may not have had a choice in the matter entirely. But in his defense, he did have a lot thrown at him without time to absorb it. So while he did have a right to be confused and upset, he took it a little too far in my eyes. Just my opinion, so you might want to talk to a Kaiden fan for a more fair assessment.
Garrus on the other hand, has fought beside Shepard since ME1. They have shared a longtime respect and friendship so it makes sense that it can eventually accumulate to something beyond physical attraction. I'm rather fond of Garrus for being there for Shepard when she needed a friend with all that she had been through. So loyalty plays a huge part in that. The curious (or downside depending on how you see this) is the rarity of turian/human relationships. But with asari/turian pairings being quite common and since lore proves that human women resemble asari very closely, it wouldn't be too much of a leap to see Shepard with Garrus. However, there still remains a lot of awkwardness and Garrus is a little lacking in the romance department. Nonetheless, his efforts lend a level of believability that so many human relationships often play out that what happens between Shepard and Garrus becomes more poignant and less soap-opera in their dialogue. There is evidence of deep feelings, but it's not spoken out as much.