Colored Coins etc. make it much harder to know how much value we need the blockchain to protect. The fact that these values are essentially "hidden" from the protocol means we can't tell what we need to do to maintain any kind of parity with them.
One popular (and possibly correct) view of things is that in the long run the cheapest available price of electricity times the amount of electricity spent per block, will approach the value of the block reward in a PoW system.
that's perhaps the asymptotic value of a block reward in a PoW system- we will always have secondary costs although they will theoretically get lower as time goes by. But really can we predict much of anything in that time frame?
Right now we have a Bitcoin block reward worth approx. $12000. If this view is correct, we should expect, worldwide, to see about $12000 worth of electricity (increasingly concentrated where electricity is cheapest) expended per block by hashing rigs.
Right now transaction fees are providing a very small percentage (one third of one percent? I think?) of the block rewards.
At some point in the future, moving to transaction fees as a primary source of mining revenue, implies that each kilowatt-hour of electricity invested in securing the blockchain will have to secure three hundred times as much value (relative to its own value) from attack as it does now.
I'm convinced that's not really enough. If we stick with Proof-of-work, we're going to have to start charging transaction fees based on how much value is changing hands, because we want to buy security proportional to the value we're trying to secure, not proportional to the amount of space it takes to store the transaction. And that means the amount of value changing hands has to be visible, and that therefore Colored Coins etc will have to be more 'transparent' in terms of the protocol knowing how much they're worth (and therefore how much security we need to buy to keep them secure).
the problem of transaction fees is even more serious and I've pointed this out before.
1) it's a given that TX fees will need to increase over time
2) if they increase past a certain threshold and the use of bitcoin becomes more expensive than alternatives like Paypal, not only will Bitcoin become unattractive for users, it will become unattractive for investors, and thus there will be a collapse in price. I can't see how we can avoid this future as the computation requirements to run the bitcoin network get larger and larger. Again, NXT does not have these issues.
-bm