I have 4 toilets in the house, 3 upstairs and 1 down stairs. The down stairs toilet has a weak flush. When flushing I notice two things. First bubbles come up in bowl and the plug in tank only allow half the water to leave tank before closing.

Before going any further get a 5 gallon bucket of water and pour it into the offending toilet at about a gallon per second. If it is filling up and not sucking the water down you should get the toilet augured. Chances are a downstairs toilet gets the most use and has paper built up on the inside. As for the flapper, I would change it out with a fluidmaster bullseye super flapper. I have had the fewest problems with them over any of the competitors. If this is a cheap contractor grade toilet, you might just consider changing it out to a higher quality unit. A Toto Drake would be my general preference as it flushes well and is whisper quiet.

You prefer the fluidmaster flapper over the korky one?

I ONLY use the Korky flappers, even for specific applications.

yes... I been very happy with the korky flappers, on both newer as well as toilets from the 1960s

I do.