>Integration with the shop frontend is difficult if you're not making a theme
As someone on the opposite end of this problem (I'm in custom theme development), the client wanting to install a new app is an immediate source of frustration for reasons almost completely out of your or their control.
If your app just gives us a manual install option, that's usually the best solution for me. I can make judgments as a developer as how best to incorporate your app into my theme. Furthermore, because I'm doing it manually, I get to follow all of my version control and testing practices. You see, Shopify actually promotes some very terrible development practices (not your fault). I have to avoid that by working in development themes, storing all my code in a self-hosted Git repository elsewhere, tagging all my production deploys, and using Git to tell me what files have been changed so I can be ultra-conservative in my deploys. Why do I need to do that? Well...
Some apps have automatic installers, which try to guess what theme you're using and then install files as they wish to the current production theme. Not only is that dangerous (what if the app breaks something?), even if the app does install correctly; it usually doesn't hit the developer themes and any developer working out of the Git tree is now working with stale files. I have to pull theme exports and compare changes to reverse-engineer what was added so that we don't wind up accidentally uninstalling half the app when we change a product template or something.
Part of the problem is that Shopify is specifically designed to be both "easy to use" and give it's merchants a high level of control over their storefront. This precludes a lot of otherwise obvious solutions to this problem, for various reasons:
1. You can't use Git as a deployment mechanism because it has a terrible UX and most new merchants aren't going to figure out how to use it. Even with a non-terrible UX you still need to educate users about it's various failure modes, including merge conflicts and the like.
2. It would be nice to have standard extension points between app and theme developers, but that winds up tying the hands of both a little. Part of the problem is that any level of extensibility also either takes things out of the hands of theme developers, or requires new users understand how to implement the component. I was hoping something like the new section system (which I haven't gotten a chance to play around yet) would fix this for app developers.
If Shopify was willing to go a little bit up-market (and, given how they've become the favorite platform of Facebook scammers, they should) they could fix these problems by offering ways for theme and app developers to agree on specific extension points. This kind of ruins the whole "just edit this template to get a thing on your theme" aspect of it, but Shopify's really outgrowing what it started with IMHO.
(By the way, there's a special circle of hell reserved for page builder apps that store everything in the current production theme. I recently had to deal with a client whose shop no longer allowed them to clone their main template as it was full of literally hundreds of templates and assets from this one app. After literal hours of manual garbage collection, I was able to get it to the point where a theme clone merely took 20 minutes rather than failing outright.)