"Those that fail to learn Magento are doomed to reinvent it, badly."
Performance on Magento is a problem on shared hosting, however, on a modest virtual server, with caching on, there is no performance problem. With added tools, 'Varnish', 'Nginx' etc there is scalable performance. It works.
It is a pity that shops cannot be simple with a simple customers table, a simple products table, an orders table and blindingly fast performance. However, the Magento started from this (with OsCommerce), realised the problems/limitations and built a far more sensible system with the best programming methods. Despite their great work there are plenty of developers that think they can write a web shop in a weekend and bolt on requirements to it as needed. Tempting these 'noddy carts' are, they are not full featured or extensible in a modular fashion, as Magento is, therefore they are generally a complete waste of time.
I don't think that Magento documentation is as big a problem as you imagine. There is 'network effect' with Magento hence, a lot of the 'missing documentation' is Google-able.
Initially the layout engine and the 'millions of files' seems confusing. However, it takes a while to learn how this works and to get a few re-usable resources of your own. I think it is better to learn the Magento way of doing things, with modules, layout xml and MVC methods. Thinking you can format Magento blocks any better in a CMS such as Expression Engine and use Magento just for the backend will put you on a hiding to nothing, to end up with a fairly useless setup that isn't going to go anywhere.
