Capturing

Alternatives

• Mechanical ways of capturing and holding animals: Cages, boxes, sacks, traps, manacles, nests, nesting boxes
• Organic representations of life: Eggs, seeds, fossils
• Fantastical ways of holding animals: Gemstones, geodes, flasks (could be sucked into the flask through a kind of spiritual vacuum cleaner)
• Artistic representations of life: Collectable cards, statuettes, paintings, photographs
• Ways of storing information: Floppy disks, CDs

Flasks

• Candied Flask: Upon capture, the tuxemon increases in level by 1.
• Flavoured Flask: The tuxemon's positive taste changes to the one specified by the flask
• Quick Flask: If the capture fails, you don't lose your turn (but the flask does break as normal)
• Friend Flask: A held item. The active tuxemon attempts a capture at a certain point (no action required)
• Lavish Flask: The capture has a higher chance of succeeding.
• Hardened Flask: Doesn't break on a failed capture.

Containment (Hikari)

Containment: Mostly because the concept of 'spirits' rather than flesh and blood creatures I'd actually looked to the cartoon 'Danny phantom' and how it uses basically a thermos to vacuum up the ghost of the week.

Instead of a bunch of tiny pokeballs, you get a thermos or jug or something of the like that you dump captured critters in. This only does final containment rather than capture though, so you would still need to buy 'regular/great/ultra balls' to catch things. However those actual capture devices break after each use (one thing I hated about pokeballs. If you fail a capture why not pick the balls up to reuse?)

Thinking they should be called bottles. Not beer bottle shape, but still bottly shaped.

Anyway the thermos/jug can only hold so many creatures, but you can plug it into a device in healing houses to free up space. Those creatures are tagged as 'yours' by whatever this system is called so that they can be called back to you at need.

Think of the inside of the ghostbusters containment system. Its own world where these things can move and interact. Sure they aren't generally all that smart, but it keeps them less agitated than keeping them stuffed in jars.

Plus it gives potential for you having to go in yourself using special gear.

Binding (Tamashihoshi)

Binding a spirit onto an object, like the soul of the younger brother in Full Metal Alchemist or the djinn bound to objects in Magi and the Labyrinth of Magic the djinn. Trainers would carry an individual object in which the spirits are bound. There could be a "easy to attach" spirit container the cathedral sells, where you can bind tuxemon without having great skill. (Probably works only on weak tuxemon though).

You could do this subtly by having different trainer sprites show different objects - without spelling out that this person's umbrella is their binding object, that person's amulet is their binding object. etc.