Some Spirits to keep an eye out for.
Zygarde 50% - It is a Green Novice Spirit, but it can be enhanced into a Legend Rank Zygarde Complete that gives 2 Slots and Critical Health Healing.
Young Zelda(Ocarina of Time) - A Blue Advance Spirit. Enhancing her will make her a Legend Rank Adult Zelda with 2 Slots and Assist Killer.
Skull Kid(Ocarina of Time) - A Green Advance Spirit. Enhancing him will make him a Legend Rank Majora's Mask Skull Kid with 2 Slots and Lifesteal.
Maria Renard - A Green Advance Spirit. Enhancing her will make her into an Ace Rank Maria Renard(Symphony of the Night), but her Power will rival that of Legend Rank Spirits, as well as give 2 Slots and an Additional Midair Jump.
Elincia - A Blue Advance Spirit. Enhancing her will make her into a Legend Rank Queen Elincia that gives 2 slots and an additional Midair Jump.
Bulborb - A Blue Advance Spirit. Enhancing it will change it into the Legend Rank Empress Bulblax that gives 2 slots and Greatly Enhanced stats after eating food during the battle.
This is a good post, I'll have to keep these in mind.
Here are some more upgradeable Spirits worth looking into
Masters
Lyn [Ace] → Lyn (Blade Lord), I'm pretty sure she's one of the best. Two slots with Critical Hit ↑↑; Red
Zero (Zero Buster) [Advanced] → Zero (Z-Saber) - Two slots with Weapon Attack & Move Speed ↑; Red
Shadow the Hedgehog [Ace] → Super Shadow - Two slots with Undamaged Attack & Speed ↑; Red
Giratina (Altered Forme) [Ace] → Giratina (Origin Forme) - Three slots with Shield Damage ↑; Grey
Midna [Ace] → Wolf Link & Midna - Three slots with Dash Attack ↑; Green
Baby Mario [Ace] → Baby Mario (Superstar Mario) - Three slots with First-Strike Advantage; Grey
X [Ace] → Full Armor X - One slot with Super Armor; Green
Aces
Tsubasa Oribe [Novice] → Tsubasa Oribe (Carnage Form) - Three slots with Jump ↑; Blue
Metal Gear ZEKE [Novice] → Sahelanthropus - One slots with Metal and Giant; Blue
X Parasite [Novice] → Nightmare - Two slots with Lifesteal; Red
Groudon [Advanced] -> Primal Groudon - Two slots with Fire/Explosion Resist ↑; Red
Chun-Li (Street Fighter Alpha) [Advanced] → Chun-Li - Three slots with Physical Attack ↑; Green
Revolver Ocelot (Metal Gear Solid 3) [Advanced] → Revolver Ocelot (Metal Gear Solid V) - Two slots with Shooting Attack ↑; Green
Boom Boom [Advanced] → Boom Boom & Pom Pom - One Slot with Hyper Smash Attacks; Red
I also have these spirits I haven't upgraded yet
Ganondorl (Twilight Princess), a Red Ace with three slots, presumably he enhances into Ganon (Twilight Princess)
Ray Mk II, a Green Advanced Spirit, with three slots; I assume he enhances into Ray Mk III
Geo Stelar & Omega-Xis, a Grey Advanced Spirit with three slots, I have no idea what he'll turn into.
And here's a few you can get through Summoning.
Dunban [Ace] - Two slots with Sword Attack ↑; Blue; obtained by combining Reyn and Fiora.
Dr. Eggman [Master] - Three slots with Electric Attack ↑; Green; obtained by combining Dr. Crygor, Tamagon, Chansey and two other Grab Types.
Raiden [Master] - Two slots with no skill; Red; obtained by combining Solidus Snake, Rosemary, 3 Attack Types and a Neutral type.
Xander [Master] - Three slots with Sword Attack ↑; Red; obtained by combining Leo, Camilla and Elise.
Protoman [Master] - Three slots with no skill; Blue; obtained by combining Dr. Light, Roll and a Shield Type.
Daroach [Enhanceable Ace] - Three slots (unknown skill), Red; obtained by combining Count Canolli, Mouser and two Neutral Types.
Isaac [Enhanceable Ace] - Three slots (unknown skill); Green; obtained by combining Garet, Mia and Ivan.
I haven't gotten Xander, Protoman, Daroach and Isaac yet, so I don't know how good they are.