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I have several colts for each generation but they all serve a purpose for different lines. But here's how I narrow it down for each line.

I cull by paper level first:
2nd gens must be B or A papered depending on if foundation sire is C or B papered.
3rd and 4th gens must paper A.
And 5th gen+ must paper *Star.
In addition to this, ALL colts must paper superior or be boosted to test superior to sire.

After that I cull by body type. I'm a warmblood breeder so unless there's a light or heavy colt with the genes I want, they all get the snip.

Next I cull based on genes. If I have a colt from an Ice line or macchiato line or any other line, and they don't have that specific gene, they get the snip. I have only made one exception to this rule with my Ice 4 line.

Also, for my 2nd gens, if I have an A papered colt out of a C papered foundation, I usually don't even bother papering that studs colts anymore unless there's one that's really desirable. I will usually snip all colts from then on. (For example, I have gotten an A papered 2g from my Snowflake foundie, my Macchiato foundie, and 2 from my Ice 4/Ice 7 foundie, one with ice 4 and one with ice 7). So I typically just snip all their colts or sell them back to the game now unless there's that special one that I just have to have lol.

And if I still have some colts left, I will look at PTs and go towards who has a higher PT. All this usually helps me narrow my colts down to a small handful each season (usually between 3-5). And personally I think its ok to have a few colts for each line (lol I have four 2g macchiato colts and i'll probably keep more next season and every season after). Hope this helps!

I have a similar process as well.

Obviously anyone who doesn't pass BA is gelded and culled.

Then I paper everyone. I'm only starting on my 3rd gens now, so I cull anyone who doesn't paper B in 2nd gen and anyone who doesn't paper A in 3rd gen (for regular lines), and anyone who doesn't paper A in 2nd gen for superior lines.

Then I comparison test all colts against their sires - anyone who's not superior is culled.

Then I comparison test colts for each line against each other. These aren't always siblings as I tend to have a few foundation studs for most of my lines, but I don't discriminate at this point. I pick one colt and compare all the other colts against him, culling anyone who is inferior, until I find someone who's superior to him. Then all the as good as colts get culled as well and I move on to testing all the remaining colts against the superior colt until I find one superior to him, and so on and so forth. Eventually you get left with a bunch that all compare about as good as the colt to whom no one is superior.

From there if I'm lucky (I almost never am) I'll have narrowed it down to a manageable number of colts. Since that rarely happens, I usually have to figure out some way to cull down further (or get lazy and just have too many colts!).

As others have said, if you have specific genes or heights/weights for your lines, you can cull based on those criteria. You could also cull based on consistency.