The line going through micros is not the issue; the issue with micros can be the knot size and clearing it cleanly through the guides. If using leaders over about 15 with braid over about 20 you'll need to learn to tie small knots for braid to leader. That can be handled, so it's not really a con as much as a caution.
Because micros have lighter weight, the recovery-from-deflection speed of the rod is less affected than it is with heavier guides. Theoretically, this should lead to longer casts and in my opinion, increased sensitivity. Another factor leading to longer casts in my opinion is that the line is constrained to a much smaller profile as is passes through the air. It's more like a small cylinder passing through the air rather than loops of line passing through the air.
Bottom line, micros make a lot of sense for certain applications. I use them on every rod I make and have no rods left that do not have micros. On baitcast I usually use runners of 5.5mm, and on spin, usually 4mm. I do have baitcasters with 4mm micros , and they work just fine.
When I first started building I bought a very nice and pricey Loomis spinnerbait blank and made my first casting rod on it. Another builder, mistaking the type of rod I was building, recommended guides much too large, and I didn't know the difference, so built it. Didn't like how it fished, and realizing my error, rebuilt it with what would be called traditionally sized casting rod guides. Still didn't really care for it. Then micros came into popularity, and I rebuilt it with a first guide of 6mm (Fuji RV6, a tall 6mm double foot), and the rest 5.5mm micros. The rod finally felt right.