we did a 16S RNA analysis using MiSeq kit version 3. This kit makes paired-end reads with a size of 300pb. By merging both reads, we can cover 535 pb of region V3-V5.
As you can see in the following plot, qualities of reads are really bad after the nucleotid 250.
Is it normal ? Perhaps the strategy prefers reads lenghs to the quality ? Did you get something similiar with the same kit ?
As pointed in the comments, Illumina's problems with MiSeq v3 kit and 2x300bp are known and old, see for example here and here. Informally, (at least some) Illumina technicians will tell you to stay with 2x250bp, I am not sure if someone at Illumina said so on record.