Full on 100% pixel-by-pixel design might take up too much bandwidth and space for slower connections/systems - at least from what little insight I have, I might be wrong. Also it may invite immature designs (you know what I mean) from trolls.
A system similar to MC Banners may be better, with set patterns and overlays that can be combined in different colors.
Couple effects I can quickly think of:
Redstone (Modifier) Increased catch rate on the first turn during battle (3 levels, requiring 50 redstone each) 2* Catch Rate, 3* Catch Rate, and 5* Catch Rate
Glowstone (Modifier) Increased catch rate on Shiny Pokemon (1 level, requires 25 glowstone), +3* catchrate on shiny pokemon
Steel (Material) Higher base catch rate (1.2*)
Diamond (Modifier) +1* Catch Rate | 3 levels
Emerald (Modifier) +50% Catch Rate
Paper (Material) -3* Catch Rate, but gives multiple modifiers to the ball
Regardless of material combos, catch rate can never drop below 0.5*
So using a couple of these; you got;
Basic catch rate all tinker balls start at = 1* + 2 Modifiers
+ Paper lid | -3* + 5 modifer = We're at 0.5* total + 7 modifiers
+ Steel bottom | +1* = We're at 1.5* + 7 modifiers
+ Glowstone | +0* -1 Modifier, +5* if shiny = We're at 1.5* if non-shiny, 6.5 if shiny +6 modifiers
+ Diamond*3 | +3*, -3 Modifiers = 4.5* if non-shny, 9.5 if shiny +3 modifiers
+ Redstone*3 | +5* if used on first turn = 9.5 if non-shiny, 14.5 if shiny, assuming it is used on the first turn, same catchrate* as above if not +0 modifiers
+ Modifier (Base Tinker's Construct item which gives +1 modifier, costs a nether star so it's hard to get, especially with pixelmon in mind) = 1 modifier
+ Emerald | +50%*, -1 Modifier = 14.25* if non-shiny, 21.75* if siny, assuming the ball is used on the first turn of battle + 0 Modifiers
So yeah, balls CAN get pretty OP, but think about the fact that it could still theoretically fail, resulting in your wasting all these materials on a SINGLE ball.
I'd stick with the purely cosmetic version FoxKid originally suggested. That's much more likely to happen.