My recommendation: Minecraft, modded via FTB or Tekkit.
Spore, Creatures, and Pokemon all contain elements of breeding and/or collecting. It sounds like she enjoys games that incorporate discovering, and researching. There's even a bit of "completionist" evident in that list - the desire to build a checklist and play until all the boxes are ticked - the pokemon "gotta collect 'em all" mentality, as it were....
Your genres lean more towards survival and engineering elements. Gathering resources, then planning a system that will efficiently utilize those resources (and therein lies the puzzle).
Since minecraft hit the public scene, it's been a goto game for a wide variety of people. It contains many of the classic gamestyles: action/rpg, puzzle, casual-play, strategy, shooter, simulation, all rolled into one. Yes, the graphics are a throwback to the late 80s/early 90s, and certainly won't stress out any video card made in the last 5 years (well...at first, anyways!).
If you (or her) are unfamiliar with the game, I recommend taking a look at some of the videos by YouTube personality Direwolf20. He plays the game both single-player and multi-player, and provides step-by-step guides on using several of the different mods that are out there. In particular, the following mods might be of interest:
* Bee Breeding / Apiculture - Through the gathering and breeding of bees, you can create a variety of new species of bees, each with their own attributes. Different bees will create different resources by way of honeycombs, pollen, and other bee-like products. Advanced apiculture allows the bee-breeder to genetically build bees with desirable attributes while removing undesirable attributes, creating a gaming environment very reminiscent of spore/pokemon.
* Tree Breeding / Arboriculture - As with Bee breeding, tree breeding allows the player to breed and discover new types of trees. Each tree has a different appearance, different colored wood, and several offer food or nut production. While not as complex as bee-breeding, it can be of interest to many people.
* Thaumcraft - This magical mod is built around the concept of aspects: the elements that make up the world around us. From the basic elements (fire, air, earth, water, order, chaos), one can derive more complex elements (life, death, light, power, etc). Through research, one can discover the different aspects that make up any block, item, or entity that exists in the game, and learn how to create new magical items from those basic aspects. Thaumcraft begins with a book that provides a great tutorial on how to get started, as well as a checklist of all the different things that can be researched. This mod is actually more "alchemical" than "magical", as you soon find that if you mix fire with energy, you can create a glowing ball of light or a bomb with destructive power - and there's not a whole lot "magical" about that. Again, this will appeal to both the researcher and the collector alike.
* Morph - This mod is generally more cosmetic than functional, but it revolves around a basic premise: once you kill something, you can morph your appearance into that thing. For instance, kill a cow, and you can change your appearance to that of a cow. You can easily change your appearance at any time with no restrictions. Some morphs provide special abilities (bats can fly, squid can swim), while some come with distinct disadvantages (don't morph into a zombie or skeleton in the daylight). Cosmetic, but fun.
* Mystcraft - Through the use of symbols collected throughout the world (or discovered), the player can write a book that defines a brand new world. Attributes of this world are based on the symbols used, and missing symbols are automatically filled-in, which can lead to instability of the new world. You can create a perpetually dark waterworld, or a forest which experiences blue sunsets. Some worlds have tendrils of wood or glowing rock that snake around it, some are rich in minerals. It's all based on how you design it. Don't forget to take a linking book with you when you enter, or you may not be able to return home!
* Twilight Forest - This mod creates a new mystical realm, full of rams, deer, and mysterious trees. In the depths, you can find mazes full of minotaurs, or you can find a cave guarded by a fearsome hydra. If minecraft is a page of out of history, the twilight forest is a page out of mythology.
These mods are specifically ones that I think may appeal to your sister. As for your game style, there's plenty of machinery, computers, and other devices that you can create, or teach other machines how to create. There are caves and dungeons to explore, enemies to fight with swords or bows, and trees and rocks for gathering. I'm sure you'll have no problem finding something to do.
Teamed up together, you can each focus on your specific interests - together, you can explore the world, and each of you return home with your treasure. Bees and new saplings for her to experiment with, iron and new crops for you to figure out. You can work independently (or cooperatively) to build your own house(s) - whether it's a brick house on a hill, a door at the front of a cave, or you can hollow out a large tree and do the Swiss Family Robinson approach.
I'd be happy to provide introduction or assistance with regards to these, or any of the other, mods that you find interesting. Just give me a holler.
In addition to the above mods (which are all included in the Direwolf20 mod pack, available through the Feed-the-Beast mod tools), you might also find these interesting:
* Milllenaire / New World - This mod features numerous human races from different cultures. After finding one of their villages, you can help them grow by supplying resources or defending the workers in the night. As you trade with them, they will become more familiar with you, and may offer you an official place in the village, even your own house.
* Hexxit - This game pack is available through Tekkit (a different Minecraft modding community), and presents a more combat/survival aspect to the game. You will find castles filled with skeleton knights, pirate ships, and towers full of treasure. You will see elephants, giraffes, and even Chocobos (Final Fantasy series) roaming around the plains. A truly unique experience.
* Also on the Tekkit site, you can find modpacks that feature other genres, including pokemon, military themes (compete with guns and rockets), zombie/apocalypse, spacecraft, and other genres. The modding community for minecraft is quite large, and there are mods out there to customize the experience to whatever suits your fancy.
Sorry for the length, but if you made it this far, congrats! The game is only about $20-30, but the replayability is VERY high.
If I've totally missed the ball on her (or your) interests, I apologize. Any clarifications you can provide may allow a better (and hopefully shorter) recommendation.
