Your design is coming along nicely. Eagle is a very useful tool,. eh?
Some random ideas for you …
Why not the best of both worlds? Pads in-between a socketed, raised module’s pins and above and below – including the pre-routed LCD pads? You get about 11mm clearance if mounting the module atop standard female IDC strips (like the Arduino has.)
As already stated by @spydrop, doing this has the advantage that the builder only routes to the pins they are using, freeing up the otherwise pre-routed pads for whatever else they might want. It has the obvious disadvantage that, well, they have to route those pads themselves, consuming precious new project excitement reserves.
Another idea is the one of replicating the size, shape, hole positions and pre-existing routing linkages of the little breadboard that the core comes with – maybe adding things like your LCD connector strip on additionally. Users then get to build something on the breadboard, getting it working there first and then transfer it (more tidily) to your PCB proto board, in exactly the same configuration.
Or do both!
You could even get V-cuts made on a larger pad array design, allowing unused sections to be easy snapped off and used for other projects, perhaps. (Not sure if OSHpark does V-cuts, though?)
Pros and cons … “Lots of ways to skin a cat!”, as my Grand Peppy used to always say. Oooh!
Re OSHpark and costs … I understood that they price boards by the sq. inch, not paying attention to any maximum side length for pricing breaks. So the shape shouldn’t really affect cost much. But I may have that wrong in my head? I only discovered them a couple weeks back and am waiting for my first boards. Yummy.
Meanwhile, for slightly larger numbers of 2-layer boards of around this size – like ten – you will probably find the PCB Prototype service at iteadstudio.com considerably cheaper, per board. I think the last 5x5cm boards I had them do were US$16, including shipping – for ten. So $1.60 each, landed. I have used them many times, with only ever the cheapest registered post delivery option and always been very happy with the results. Total delivery time is roughly the same – ITead being China based and me being in New Zealand.
Don’t get me wrong. OSHpark rocks for new prototypes or one-offs – especially 4-layer boards and with ENIG (gold plating) as standard. Wow. How do they do it?! Very cool.