I'm gonna divert a bit from actual tips to traps you should, at least, be aware of.
The mention of "mysterious eyes far in the background" brings to mind a concept from Genetics. Here's the Wikiepedia page for it:
http://en.wikipedia.org/wiki/Genetic_drift
Genetic Drift seems a contentious issue in real-world genetics because, for most large populations, it arises from your statistical methods and is not a "true genetic" operation.
In a nutshell: genetic drift is the tendency of a given trait value to either entirely disappear from your population, or become spread throughout your entire population. It effects ONLY those trait values which have no effect upon fitness to survive and reproduce.
But, in breedables, such as KittyCatS, Genetic Drift is a very real effect: and it's caused by YOU! There is nothing anywhere in any breedable's programming which implements Genetic Drift; but all will exhibit it.
So why does Mysterious Eye Shape bring it to mind? Well, quite simply because, while two-value traits such as Mysterious Eye Shape and Small Pupil are easy to obtain, the fact that there are only two values actually makes them the most likely to be lost.
So, OK, I'll turn this into a tip ...
Even if some traits or trait values are not important to you, today, PAY ATTENTION TO ALL OF THEM, ANYWAY.
Sure, you're madly rushing to get that Seal Lynx. And, yeah, you're planning on adding Peach Belinni Eyes to it .. later. But some day you'll want to have perfect eyes. So, if you were not watching ALL traits, in ALL lines, you can find, when you finally decide to look, that you don't have ANY cats carrying Mysterious Eye Shape, or Small Pupil.
Didn't I mention keeping a "seed bank", earlier?
This effect is why I actually LIKE that the KittyCatS team has never added a third value to those two traits. It's a hidden trap for the unwary!
When counting traits ..
There are 18, not 9!
You see a 9-trait cat. I see 9-Shown, 9-Hidden: total 18. Actually, I count fewer if I'm sure that a hidden is the same as the shown! So the best I actually count for a 9-trait will be 16 because I'm quite positive that perfect eyes always hide perfect eyes. Yes, that means a Twinkle will count less than an Illume hiding Twinkle! But that's A Good Thing if I'm interested in exposing Twinkle.
Often times, when trying to decide which mate is "best" it can help to count not just the shown traits, but the additional, hidden, ones you can prove are laying behind those shown "generic" values you're not counting.