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Do you ever choose a Captain over a Chapter Master other than if you don't have the points for a Chapter Master?

Do you think that a Captain should differentiate from the Chapter Master in a positive way? If yes, how?

Could a Captain have access to or have some skills that a Chapter Master don't have?

I always choose a captain for the command squad. No other reason. A chapter master unlocks honour guard that I think are a bit, 'meh'.

If it was either or I would always pay extra for the master.

Just can't pass up 5 guys with specials.

Only two possible reasons to choose a captain. One is points - which can actually matter if you're playing a much smaller game. A 250 point Chapter Master would dominate a 500-750 point game, but you wouldn't be able to bring much else.
The second, and more important reason, is that a Chapter Master doesn't unlock a Command Squad. Honor Guard are great combat units, but a Command Squad is definitely more versatile.

Cost is a big one. A properly equiped chapter master costs a lot of points.

Small games don t always need the top level HQ, plus space marines most basic units are pretty expensive, not always room for one.
Sometimes you just need a captain, or chaplain for example.

Fluff bunnies like myself might choose a captain purely for army fluff reasons. I personally never field a chapter master if the game is under 1850.

Heck, for most games I rarely even field a captain, normally going with a Librarian at 1500 points. Most of my marine armies are heavy on infantry, using big points generally for centurians, or drop podding sternguard, or on special occassions, a LR filled with TH/SS termies. This leaves very few points for HQ, so its often the cheapest I can get by with while still getting something useful, so it always ends up as a Librarian.

Ah yes I forgot that only through the Captain can the Command squad be chosen. Are you okay with this - that the Captain hasn't got other benefits than this?
I can't come up with something which a Captain could have and which he suddenly lost if he was to be promoted to a Chapter Master, but it would be nice to have other incentives to choose a Captain than the two which are mentioned.

Also great that you choose a Captain because of background - my kind of way to play and choose armies!

Well, he's cheaper, which can be a plus, but, in all seriousness, why should a Captain have perks over a Chapter Master? The CM is the upgraded version. The upgrade gets the perks, Captain is the base version.

The only real reason I can see is they want a cheaper combat character, but that's about it.
They aren't even the sole generic HQ that unlocks Command Squads, as Librarians and Chaplians do that, too, and Librarians are cheaper and generally more useful than Captains.

If you have a Character that isn't on a bike, like Tyberos or Calgar or Sevrin, and need something that'll open up our best troop option, you buy a cheap Captain on a Bike and accomplish that mission.