Is a disadvantage really a disadvantage? It depends on how you look at
it.
In most point-based RPGs like GURPS or the Hero System,
things which are disadvantageous to the character have a negative
point value: in return for being scared of spiders or short-sighted,
you get more points to be awesome on other respects.
I see this historically as part of the general move away from an
adversarial GMing style of the late 1980s and early 1990s: the
player's reaction to that, to a GM who will remorselessly use any
lever to punish the character, is to build a character who is an egg,
all smooth surfaces and no handles. You can't put my Aunt May in
danger if I don't have an Aunt May. Once players have been thus
traumatised, it's hard to get them out of that mindset again, and so
the negative character point value of disadvantages serves as a bribe
to get them to make a character more interesting. (It's also a puzzle
for optimisers: how can I use the points gained from a disadvantage to
get some other ability which will allow me to make the disadvantage
irrelevant? But I diskard such people.)
I'd like to consider an alternative model. Every trait that goes on a
character sheet, positive or negative, is a way of demanding GM
attention and spotlight time. The positive ones are obvious: I am the
sword master or the genius lock-picker, I can solve this problem. But
the negative ones can works similarly: the team will fly to Algiers,
oh no it won't because I don't do planes so now we'll need to build a
new plan around me.
(Parenthetically, I gather that this was the genesis of the FATE
system: to describe traits neither as positive nor negative, but to
make them broader, so your "struggling space captain" trait can be
both positive (I know how to run a spaceship) and negative (debt
collectors are after me) depending on the situation.)
And this I think is why every game I've met that has disadvantages
like this has a limit to the total one can get. If my character
could have all the disadvantages and all the advantages, then in any
given situation they'd have some way of requesting special treatment.
Mathematically, if I have A points in advantageous traits and D points
in disadvantageous ones, GURPS says that A - D must be no greater
than the point budget; but it also caps D. Indeed I wonder whether
one might usefully put a cap on A + D, the amount of special
treatment that a character may demand.