>cannot happen due to a combination of trademark and copyright law

There is no need to redistribute anything, as you've said yourself: pretty much every jailbreak tool comes with Cydia. This hypothetical new tool just needs to remove the installer part of Cydia, which would be legal. Also, advertising "compatibility with another product" is a pretty gray area of trademark law, and lawsuits are expensive- they can bet that you might not want to get embroiled in a lawsuit, where you have everything to lose and they have nothing to lose. It's not a completely far fetched idea.

> what you are describing is weaker branding

Let me clarify my points about branding: with separate branding, I was proposing "weaker combined branding, stronger individual branding". I am not arguing that they are not tied together economically and legally.

> You make it sound like separating them solves this problem, but them being accidentally separate is what caused this problem in the first place

Oops, I think you might have misunderstood my examples. I wasn't saying that separating the brands make it harder to compete against. I was saying that combining the brands to reduce competition is just as effective as using DRM to reduce piracy- that is, not at all. A lot of game studios nowadays, instead of adding DRM to combat piracy, release games without DRM. Similarly, instead of combining the brands in an attempt to reduce competition, just embrace the fact that it will happen no matter what.

In formal logic, let p be "separate brands", and q be "more competition". You are saying "p then q, so it is better to not-p"; on the other hand, I'm trying to say "p AND not-p will still lead to q, and p has good effects, so just do p". Hopefully the previous sentence made sense, haha...

> and pulling it into the forefront as the development tool

I feel like this is a "mere" advertising problem, and not directly related to its branding. Currently, you're trying to make Substrate more popular by combining it into the brand that the Cydia installer has. Alternatively, you can make it more popular by creating another brand and advertising its power through that: say, create "Aidyc Substrate" ("Cydia" backwards) (ok that's a shitty name but w/e), and building on that and advertising that. Both methods could work in the end.

Apple themselves can show us the power of two individual brands that rely on each other while tied at the hip: "iPod" and "iTunes"! Creating separate brands do not take away from the individual products. Can you imagine if Apple decided to call both the music store and the device "iPod"? Separate brands, intrinsically tied together legally/economically/user-experimentally, and provides a great example of what could work out. If both products are strong, they only reinforce each other away from competition.

-----------------

As an humorous aside note, I just realized that since you have a monopoly on jailbreak tools, and SaurikIT is a "legal" company, someone can sue you for anti-monopoly for bundling stuff together. It would be extremely unlikely (although quite funny from a bystander perspective, probably less so for you) for the courts to pull the Sherman Antitrust Act on you like that, though.