As others have indeed already suggested, instead of aiming to punish blobbing/wide play, perhaps the better alternative and best option is to add bonuses and encouragements to "playing tall".
One of the big issues obviously is that acquiring development through developing is simply less efficient than grabbing new clay/conquering (even despite religious disunity/separatism and autonomy). Although farmlands, luxury trade goods, an Orthodox icon, Florentine ideas, economic ideas, and the economic+quantity policy can mitigate this, most of these options are either situational, limited to a specific nation or religion, or not viable for most parts of the map (have fun developing in most of Persia, the Alps, or the Himalayas).
Perhaps there could be a development cost reduction tied to either prosperity, or a similar mechanic which goes up by staying at peace (or at least avoiding wars in your homeland) and spending money on local improvements of state provinces (buildings or some other new mechanic - ala opposite of corruption, so perhaps a "pay for national improvements" slider or something).
Perhaps by having high prosperity (or a high level of the hypothetical new mechanic's currency) your nation could not only have reduced development costs, but faster local autonomy reductions, cheaper and faster regiment/ship recruitment costs, increased manpower, tax and trade modifiers.
You could also perhaps receive a series of positive events for keeping your "national prosperity/attractiveness (as another poster suggested as a name)" high, that would boost your diplomatic reputation, maybe even grant an additional diplomat, merchant, colonist, and/or general/admiral, and decrease institution embracement cost (and similarly increase the rate of spread). These events could perhaps make other nations more willing to ally or royal marriage you (and maybe increase the chance of getting personal unions for Christian nations, and maybe have piety/mysticism boosts for Islamic nations - and religion-specific boosts for other faiths too).
Similarly, keeping your prosperity/attractiveness higher could allow you cheaper-higher-level advisors and maybe even a higher chance of rolling more skilled monarchs.
Additionally, this hypothetical mechanic could, as also suggested earlier, be tied to your development/province ratio, and both religious and cultural unity (with culture unions and promoted cultures giving no or only a very minor penalty).
All of these things would presumably make playing tall more attractive, although granted it's still a long way to making tall play "more fun" since even doing this would mostly just involve sitting around developing, fighting minor wars over humiliation, ducats, prestige, treaty-annulling, and returning cores, with a small bit of conquest mixed in. Sure, just clicking events and "develop province" isn't exactly as much as coordinating armies in huge wars, but at least it's a start to make it a bit easier if a player chooses to focus on tall play instead.
