You and me are both in the same boat. I tried most open source CMS platforms and shopping carts.
After days of installing and testing everything I could find I wasn't very satisfied with anything really. If I HAD to choose a CMS it would be Wordpress only because there are many themes and plugins to save me time for rapid deployment. For ecommerce my final pick was opencart. None of these will ever function or look exactly as I want or the project requires without re-engineering the code and templates. If you go too far modifying the core you can't upgrade in the future.
The problem with all of these systems is that they try to cater to as many businesses and scenarios as they possibly can. A lot of the code is bloated with way too many features that you will never use. Stripping down the code before deployment is not possible because of future upgrades. Also I found that updating or creating new themes for these systems takes longer than rolling out custom.
With that said I created my own ecommerce solution. I have deployed two high traffic e-commerce businesses coming off of ShopScript and CSCart software and the speeds of the websites increased on average by 50%+.
Now I am in the process of creating a simple CMS system where customers can edit the content of the website but not the layout. This will ensure the highest performance on my end and still allow the client to change copy on the site. This super simple and efficient system runs of 3 tables in a mySQL database.
So as I always say, custom is the only way to go for e-commerce. For static or informational websites wordpress is ok only if the client already likes one of the templates already available on wordpress. I setup the software, create the mail boxes in postfix and give them a overall lesson how to use it. I charge for add-on services like adwords, hosting, e-mail, domain costs and maintenece for these clients. I very rarely go into the templates and modify any code. I call those ME TOO sites. (as in oh I have a wordpress site and love this template... me too!)