I would like to have a way to add user created instruments. This would include instruments not yet in existence or instruments no longer commonly used instruments. I would also think it would great to have a spectral analysis tool to record overtones and waveforms to more accurately emulate the sound of a particular instrument.

What you look for is maybe granular synths with additive synthesis.
 
Waves Codex might be interesting:
http://www.waves.com/plugins/codex#codex-synth-in-depth-tutorial
 
Not sure if synthesis is additive though, did not look. It look like regular subtractive filter envelopes.
But really new way of doing things.

Are you looking for a platform to create instruments? If so, then Reaktor by NI is the logical choice. It's been in development for several years now, and is a mature and stable platform. A lot of resources and tutorials are out there for designing any type of synth, effect, or combination. Just a look around the library is rather intimidating.
 
https://www.native-instruments.com/en/community/reaktor-user-library/