This is the story of my somewhat obsessive process in keeping my pokémon collection tiddy. TL;DR: I keep a row of 3 for each pokémon, with mostly highest IVs, and lvl 20 and above.
When I started playing I had zero experience. Like any newcomer I thought CP were everything. Based on other false assumptions, I thought one had to have a tiny and king size pokémon as well, so being on the collecting side, I started keeping one pokémon each size, replacing them with higher CP if any. In these days I probably trashed many valuable pokémon.
Then I learned what I had to, the IVs, the movesets and so on, and restarted my collecting process almost from scratch, labelling my pokémon based on IVs, and a/d/p for the battling pokémon. I was still keeping 2 pokémon each.
Then one day I was bored, I found out that 2 each was clumsy and didn't allow fast browsing, so I went ahead and started keeping 3 each. First I kept as many as needed to fill the rows, whatever IVs and movesets, and later replacing the low IVs with higher ones.
So today, for each and every pokémon, I have 3 of them, mostly highest IVs, mostly lvl 20 or above. If I catch/hatch an extra one, I will discard the lowest IV, and so on. Being on iOS, I must say Pokégenie is a invaluable timesaver!
Like most of us I use Pid/Cat/Weed and even Rat for mass evolutions, but I always keep an extra row of 3 for these ones, so I label the trashable ones differently to always keep 3 best Pidgey etc.
As for every rule there are exceptions, mostly for the battling pokémon, where I will keep anything with valuable movesets and IVs > 50%, even my 100% IVs Gyarados with twister (a minute of silence please)
There are stil a few holes in my collection, a few pokémon for which I still haven't found the highest IVs - I've become pretty obsessed with Muk - or some pokémon and their evolutions for which I don't have the perfect rows. Doduo/Dodrio, Machop/Machoke/Machamp are amongst the rarest. But I have all the others except Togetic, so my regional pokédex is almost complete.
Are some others as crazy/obsessive as I am?