I have a document that goes to all prospective clients, it's a balance in showing the positives but also ensuring clients are aware of the restrictions of Shopify. It's always important to realise as a SaaS there are elements that cannot be changed (checkout for example)
We use Turbo theme for clients, it's a decent regularly updated theme. With the new updates modifications are much easier from a tech point of view meaning update costs are kept down. The one off cost is $400, however it is a very strong converting theme and means most clients don't need additional apps.
Shopify have recently updated the platform allowing theme modifications using a app style system rather than needing to edit core theme files, big bonus.
For one store earlier in the year we made massive changes, things like product subtitles, custom shipping options for products, linked products (brewery and they wanted to show other products that contained each beer), gift wrap service etc.. Everything was coded rather than using Apps which saved over £500 a year in app costs.
The latest one was for a music label, apart from custom shipping options the only features we needed to add was the option to add tracks that could be listened to as well as custom tabs on product pages. Everything else was covered within the theme.
It's far from perfect, but is very much a turn key solution if setup correctly. The admin is very easy to use, the API allows for custom coded options.
Most small businesses can get away with the $29 a month account unless they need more staff accounts. Paid yearly they get a discount and get the free shipping calculator service allowing 3rd party rates (we write custom options for clients needing it)
There are a couple of tweaks that can be applied to most themes that traditionally improve the SEO but a decent theme off the shelve will be a very strong start.
Images should be named correctly, alt tags set etc... thoughts to front page product linking, top level menu items etc.. the usual stuff.
Often when migrating things like images can be named in an automated fashion with alt tags etc.. which save on a lot of work.