Losing a flag is not a glitch; it is a combination of nature (waves) and possible operator error (I DID cinch that flag strap down extra tight, didn't I ???). Meh, stuff gets dropped/lost by boat divers, too.
They're both excellent, but different approaches to diving; shore offers almost always more exercise lugging gear and with surface swims. More self-sufficient, especially if diving solo. And no charter/fuel costs. You're usually going to pay for parking at most charter spots, anyways. And you realize the true value of a compass and are more attuned to currents; otherwise you have a long walk down the beach lugging your gear which is not a fun way to end a great dive:=}.
Control: Unless you own your own boat, you might go in the general vicinity desired on a charter but unlikely the captain will drop you on the exact GPS coordinates of your favorite nearshore lobster patch.
But I'm not going to surface swim over a mile each way to reach the bugs at Anglin's Ledge for a 40 minute dve, I'm not going solo drift diving off the beach without a solid plan and reliable pick-up (good luck there), and boat diving has its comforts and relative benefits.
I love and recommend both shore and boat diving!!!