I played a Takamine until I wore the frets off of it. I now play a Taylor 414ce. Both are very nice guitars that absolutely shine when plugged in.
OP, what do you want to do with this guitar? Are you interested in playing fingerstyle folk or blues, or are you doing more chord strumming/rock playing? Different guitars tend to be better suited to one style or another. Your answer here will lead you towards a dreadnought or a jumbo size (for strumming chords) or an orchestra model (for fingerpicking). While you can fingerpick on a bigger bodied guitar, and strum on a smaller guitar, it's worth thinking about how you want to play when you make your choice.
In terms of looking at guitars, knowing your budget is a must. Some features to look for: All solid wood is desireable, but it comes with a price tag. If all solid is too rich for your blood, at a minimum get a solid wood top. Laminate tops just don't resonate like wood. If you want to play in a band, you might want an acoustic-electric that you can plug in to an amplifier. Even if you're not currently playing with others, it's a nice option to have. You may also want a cutaway to help you reach higher frets for solos--play some with and some without cutaways to get a sense of what that does to the tone and feel of the instrument. Look carefully for small cracks at the stress points on the guitar -- if it's been in the store for a while it may not have been treated as kindly as it ought to have been--and check for the usual issues just in case. You may also want to have someone else play it while you listen, as the way the sound projects from an acoustic means that you can sometimes get a truer sense of its tone by standing in front of the soundhole rather than sitting above it. This is important if you're spending a good bit of money, as you can't change the tone of an acoustic as drastically or as easily as you can with an electric. It all comes from the combination of wood, wire, and hands. Keep in mind that the strings may be old and thus not as bright sounding, so you may want to ask the employee at the store to change the strings for you. Don't do this if it's a $500 guitar, but if you're dropping $1500, they should oblige you.
Maybe the most important factor is the feel -- how does the neck sit in your hand? -- does the guitar respond to your playing? Does it feel "alive," vibrating and resonating with the notes? -- is it easy to fret and get around on, or does it fight you? Setups can be changed, but I feel like there are too many good instruments out there, and if it's not setup at least passably well, and they won't lower the action for you to try it out, then there are other choices that play better. If every guitar in the shop is setup poorly, buy elsewhere as that's a sign of how they take care of their guitars.
It's all about how the guitar feels to you, but there are some proven brands that you should be able to find in most big-box music stores. I highly recommend Taylors and Takamines (not been impressed with the "G" series though), and I've played some nice Martins as well. Gibson is another good brand, and I've found Ovation to be hit-and-miss. Played some older Ovations that were great, played some newer ones that didn't do much for me. Even if you're just learning, buy the best guitar you can afford that speaks to you. You want it to inspire you to play, not frustrate you.
Ultimately, choose what feels right to you. I'll offer a final, biased recommendation based only on my own taste and experience: Get a Taylor Grand Auditorium model. It's in between the Dreadnought and Orchestra sizes, so it's kind of a jack of all trades guitar, and Taylors just feel great to play. The Taylor 114 and 214 are laminate back and sides and solid top, and the 314 and up are all solid wood. The 114 & 214 sound good and feel good. The 314 is a definite step up in sound, but also price.
Good luck! Shopping for a guitar can be overwhelming, but it's also a lot of fun. Enjoy it!