Hey Vincent,
Thanks for pointing out the need for this. We have decided to start working on this app regardless.
We actually come from Magento development and that's where we have done previous Click and Collect development and it works rather well. The biggest battle you will have with Magento is scale. If you already have Retail stores then you are going to struggle with Magento in terms of cost and scalability as you will jump straight into the Mid-Level size and that will require you to implement infrastructure rather than a single server setup. If you do decide to go with the Magento route use extensions such as Turpertine (Varnish Cache) and CM_Redis (Session Storage) straight off the bat or you will have issues with poor performance, dropped and duplicate orders due to performance issues as your online comes in to line with your retail sales volume. Magento also struggles with big catalogs so if you have a lot of products you have to rely on your catalog lagging about 3 hours behind your actual changes. Also the biggest thing with Magento is avoid anything that causes a burst in traffic like 50% off sales as your servers won't cope.
With that said Shopify also has it caveats. They are however disappearing as the company and community grows. Issues we have always had are Gift Vouchers (Which are now available), Order Editting (We have just made an app for this), Cart Pricing Rules (Not Available and this is where Magento is strongest), Category Sorting and Filters (Some apps limit this but nothing that does the whole package) and Catalog Pricing Rules (Bold Apps have an app for this). Apart from that Shopify is solid, it scales like nothing else. You could have a sale giving away all your stock for free and the load from customers hitting the server wouldn't even be noticable. If anything Shopify actually gets faster the more users are on your site as it warms up the cache for you.
From a development perspective Shopify trumps Magento in every aspect. Things such as webhooks allow us to write applications that listen for order changes and then trigger events where as in Magento you need to poll on set time intervals and search for changes. Shopify API is solid and will always give a response, however with Magento we find our API calls fail most of the time as we request information from Magento but it takes more than 60 seconds to respond so it times out.
I recommend Shopify now and even help migrate our existing Magento clients on to it as it gives us some sanity. Magento seems nice from the outside and it seems like everyone is using it because it is the better system. The truth is it isn't and it gives companies and developers headaches all day long.
Anyway that's my opinion after spending years working with both systems and in the end it comes down to your exact business model and the features you require.