Government Center is easily accessed by train, so I wouldn't worry much about the commute there.
The South End, Back Bay, and Bay Village are all great options, but I also think the Waterfront, Seaport District, and Leather District should be mentioned here as well. The Waterfront and Seaport areas are truly amazing spaces to live and play, and Government Center is walkable as well as accessible by public transit. I consider this area to be where the South End was 5 or 6 years ago, as many restaurants and bars have been popping up. You'll find newer buildings here as opposed to the brownstones the Back Bay/South End areas offer, so it is ultimately what style you might like better!
Hope this helps,
Is that bars?
Or restaurants and bars?
Or restaurants and bars and entertainment?
Or restaurants and bars and entertainment and sports and parks?
That cater to a particular croud or clientelle or status?
Graduate college croud vs professional?
Blue collar vs not blue collar?
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Beacon Hill, amazing restaurants and shops, easy commute. Stable real estate economy:
North End, access to the waterfront, parks, restaurants, shopping and faneuil hall:
Also consider The South End. It is an amazing place to live and invest. Incredible restaurants and shops, and easy access to Copley, Newbury St, etc. Property values still climbing and area still gentrifying which makes it a great place to invest your money. Everything on the market equipped with a map:
Hope that helps!