It has to do with the way lithium batteries have a memory and remember the way they are charged/discharged. If your MacBook is plugged in all the time, the battery doesn’t get fully cycled from charged to discharged as it is designed to be used. And that results in the almost full charge at 98%, because the battery “remembers” not being fully cycled. You might see 97%, or 99%, but that’s the same deal: it’s almost a full charge, but not quite.
So you should run the battery down once a month or so, preferably until the MacBook goes to sleep and/or shuts itself down. That fully cycles the battery and makes the MacBook’s power manager reset itself, too.
If you keep your Macbook plugged in all the time, the battery will develop a memory of using AC all the time and the battery will not get mostly or fully discharged. And as a result, the battery won’t last as long, either in useful run time or in overall lifespan.
So run the battery down once a month; it doesn’t hurt; it actually helps with battery life. Save your documents or quit all your applications to be on the safe side. The Macbook will go into safe sleep anyway and safely shutdown, too, when the battery is completely discharged.
If you run the battery down a few times and the charge still doesn’t go above 98%, you can reset the the System Management Controller (SMC). See this Knowledge base article and find the instructions for your particular MacBook: Apple Knowledge Base: Intel-based Macs – Resetting the System Management Controller (SMC).
It’s easy to do with a simple restart while holding down some keys. I’ve had to reset the SMC from time to time on all my MacBooks and older iBooks. If you still have charging problems after that, check the Apple support site. Apple has had to issue recalls in the past for bad batteries.
Now, Apple states that “Some Mac notebooks (PowerBook G4, iBook, MacBook Pro, MacBook, and MacBook Air) may not show the battery as 100 percent charged in Mac OS X, even when the power adapter is connected” and that this is normal. They maintain that the charger and power management unit is smart enough to “not charge the battery to 100% automatically if it will add additional wear to the battery.” See Apple Knowledge Base: Mac notebooks – Battery may not show a full charge in Mac OS X. And that’s true. My Macbook only charges to 98%, but I still get nearly 2 1/2 hours of useful battery life out of it.
Eventually, you may need to get a new battery if the charge life gets low. Batteries simply wear out and don’t last forever. For each of my iBooks and Macbooks, I’ve bought at least one new battery because I use the laptops so much.
And if you do get a new battery, consider getting one from Apple, even with the extra expense. There are many OEM battery manufacturers out there, selling on their own websites and through amazon.com, Best Buy, etc., but from what I’ve found, the quality of the batteries can very widely. If you want a battery that is exactly Apple white and not an off-white color, and want the best lifespan and charge time, get a real Apple battery from Apple.

Not the greatest color match, but it works.
I bought a battery from a company on amazon.com and though it works and holds a good charge, the color is off-white, it doesn’t fit precisely in the battery bay and the charge indicator LEDs are not aligned. True, it was only $30. But it also was shipped in barely any packaging, and I’m kind of surprised it wasn’t damaged.
A friend or two bought batteries from amazon, too, and one sent the battery back and got one from Apple for quite a bit more money.
But next time, I’ll buy a genuine Apple replacement battery. I think they last longer, are much better quality, and the color will match, too.