I am looking to create a genre-spanning title that is, at its center, a visual novel, but that incorporates puzzle, skill building, search-and-find, and shop simulation elements as well.

I'll elaborate on each individual element to give a better idea of what I have in mind.

Visual Novel: I would need to be able to incorporate all of the standard features of a visual novel. The only potential problem I foresee with this are the story-affecting choices, but this is absolutely imperative.

Search-and-Find: I would like to include several different locations that vary with the in-game seasons and contain fairly mild animations (plants blowing in the wind, etc.). Within these locations, players will be foraging for herbs -- among other things -- and it needs to be possible to vary the likelihood of certain flora and fauna being available during any given visit. For example, a rare species of butterfly that will only seldom fly onto the scene. Also, I would like for player's to be able to interact with the locations with various tools from their inventory.

Shop Simulation: This one's pretty straightforward.

Puzzle: This one's a bit complicated. Imagine, for example, that a player was attempting to prepare a potion that would induce a Romeo and Juliet-esque death-like state. The may be able to accomplish this by combining an ingredient that prevents insomnia with one that stops the heart, counteracting the latter by tossing in a drop of Draught of Immortality or some such. I'll need to incorporate some sort of algorithm for how each ingredient reacts, alone and with others.

Skill Building: Again, this one's self-explanatory.

Potion Making/Ingredient Preparation: I imagine players being able to stir their bubbling brews with actual movements of the mouse, with both direction and speed variation being accounted for. Similarly, I would like for players to be able to slice/chop/smash/etc. their various ingredients.

Note: For those who don't know, visual novels are a sort of interactive fiction. The general setup is one ore more 2D characters with interchangeable expressions atop varying backgrounds and a textbox containing the story at the bottom of the screen. Usually, important scenes contain actual illustrations. There is background music throughout, as well as sound effects and, often, voice acting. Mild animations are not uncommon. The interactivity comes in the form of decisions that must be made throughout that story which effect its direction and outcome.

Just about everything you listed up there isn't that relevant when you're choosing your engine or language. There is no engine or language that will do those thing for you, so regardless of your choices, you will have to develop those features yourself.

Now, when you're choosing your engine and language, you should ask yourself these questions:
- Do I want to make 2D or 3D stuff? (3D can always do 2D, but not vice versa)
- Do I want a high-level / low-level development environment? (Usually high-level means "easier to learn, offers possibilities, but may lack a specific feature", and low-level means "you can do whatever you want, though it may be more difficult")
- Which language you prefer yourself?
- Which enginges you would like to use are available in the languages you prefer?
- Which languages can be used in your preferred engine(s)?

For example, you may find Java the most suitable language for you (you already know all the quirks of Java, you prefer OS independency etc.), so you could use jMonkeyEngine, which is written in Java, it offers great variety of options, and it's a mixture of high-level and low-level stuff.

For another example, you may know C# better than Java and you want to develop for Windows only, or possibly to 360 or Windows Phone 7. Then the obvious choice of environment is XNA. The current problem with XNA is that you pretty much have to develop your own engine, since there is not that many "full package" solutions out there, at least not for free. This is especially true if you want to make 3D game. For 2D, XNA community offers great choices, for example Krypton offers cool lighting features, and FarSeer Physics offers nice physics library.

If you don't know about the engines and languages they support, I suggest you check out this Wikipedia page: http://en.wikipedia.org/wiki/List_of_game_engines

As the game will be presented mostly as a visual novel, it will be 2D (think something like this, but with the additional features I mentioned). I would definitely want cross-platform support, as my system is running Windows 7 and I want the ability to package for both Mac and Linux releases as well. Additionally, the only language I have any experience with is Python, but it would be possible to bring an additional programmer on board if necessary. I should probably also mention that it'll be a commercial release.

I suppose what I was asking is which engine would you go with if you were making a game such as this (and with the above specifications).

With the specifications you mentioned, Java would be my way to go, since it works on just about every platform. Another possibility would be Unity3D, since it can make builds for multiple platforms as well, though it is quite costly.

I have never realy understood this compulsion to make games cross platform for indi groups. Windows covers just about 90% of the computer gaming market. So why put all that extra effort and time into 8% of the market for Macs and 2% for others. Why not just focus on getting the best game for the largest part of the market?