Granted, hitting a knee can be a problem for some. This can be minimised or eliminated if you shorten the ends of the bars.
When I returned to using bar ends, I shortened the length of the drops by c.2.5 cm with a pipe cutter. This only reduced the effective length of the bars a little since the housing of the shift lever overhangs the bars by a cm or so, and the back part of the heel of my hand can rest there. I use a small part of the heel of my hand to shift the lever downwards (the movement is tiny) & the last or last two fingers to move the lever upwards—the bulk of my hand is lying along the bar and the top of the lever. If I'm riding in the drops, other riders can't even see that I've changed gears (some have commented). But if they're close enough they can hear me change the rear cogs cos the lever makes a satisfying click when it's moved—helpful when I'm tired in the night and trying to keep track of what I'm doing.
I can honestly say that since permanently changing back to bar-cons over a year ago, I have no recollection of ever hitting a knee against the shifters. Nor can I recollect ever knocking the shifters out of position when leaning the bike against a wall.
A few BTWs:
* Of course, my whole fit & set up is adjusted with appropriate bars &c in mind, and my bike has relatively short trail (44 mm) & headstem (80 mm), so it doesn't sway much—or at all—when I'm climbing, out of the saddle or if I'm ever "grinding" up a hill (mostly I fly lightly up hills like a little bird).
* I ride in the drops more than I did when using brifters, but I think that's a good thing—more variation of hand & body position over long distances, and greater control on descents &c.
* If I'm riding on the hoods or ramps it's a simple movement to drop my hands into position; sometimes I don't even let my hand touch the drops, just flick the lever up or down (often with a whimsical flourish).
* Moving from hoods/ramps to bar con to change gear is a little slower than tapping a brifter, but not by much, and carefully watching & anticipating traffic minimises problems. For me, the advantages of bar cons that I mentioned before, outweigh this relatively minor problem.
* Bar con levers are perhaps marginally more exposed than brifters if the bike falls—but if they are not over-tightened when installed there should be enough rotational "play" to allow them to move a little when they hit the ground, minimising damage—and, as mentioned, they're much cheaper to replace than a brifter. I was recently doored and the bike fell hard to the ground at speed: fwiw, there's only a slight scrape on the bar con; the corresponding brake lever is heavily scored.
* If you have brifters and you damage the braking mechanism you have to pay to replace the gear mechanism as well; if you damage the gear mechanism. you have to replace the braking mechanism as well.
* If I were riding in a lot of criteriums or pacelines, I'd reconsider brifters. On brevets I'm mostly on my own. If i'm in a small group and I think there's going to be a problem I call out my gear changes, eg, "changing down". (It's like calling "standing" if you're in a group of unfamiliar riders.) But I can only recall doing this less than a handful of times.