All plants and fruits are rated on a percent variable, the actual value is hidden in the background and the game instead displays a generalized quality level(normal, nice, etc...) based on this percent. This can cause what appears to be a discrepancy when planting fruits/seeds as a seed sitting near the top end of a range is much more likely to be bumped up a level then one sitting near the bottom end. On top of this the ranges do not all seem to be of even size which can cause additional unevenness. I am not sure this entirely explains what you are seeing, but it likely is at least a part of it.
This is exactly what I've noticed when it comes to planting...and any time I build a house, someone is a gardener at some point.
When it comes to produce that is "Great," there is a range of Greatness. Some produce will barely be Great, while others will be astoundingly Great, and a whole range of different levels of Great in between. As players we don't see this...all we can tell is that the fruit or vegetable is simply "Great."
I'm going to use some arbitrary numbers to illustrate this. I'm going to assume that the scale is 1-10, and that the growth of the fruit itself boosts quality by 3 and the planter's Gardening skill boosts quality by 3. These are not exact numbers, and I only use this scale for simplicity's sake.
Plant 1 is Great, and is at 5 on this scale. Growing boosts the quality by 3, so this Great plant produces Great produce that is 8 on this scale. Replanting the produce boosts this by 3, making it 11 on the scale, which makes the resulting plant Outstanding at 1 on the scale.
Plant 2 is also Great, but it is at 3 on this scale. Growing boosts the quality by 3, producing Great produce that is at 6 on this scale. Replanting boosts by 3, only elevating the quality to 9, so the resulting plant is still Great. But as this plant grows fruit, it boosts a further 3, making it a 12 on a scale of 1-10, which pushes the produce into the Outstanding category (at 2 on the scale).
Plant 3 is Great as well, but it's at 1 on the scale. Growing boosts quality by 3, resulting is Great produce that is 4 on the scale. Replanting boosts another 3, resulting in a Great plant that is 7 on the scale. However, since growth boosts by 3, the resulting produce of
this plant is also Great...but is at 10 on this scale. Planting this produce will result in an Outstanding plant.
It is worth noting that these are nowhere close to exact numbers, and I don't know what the exact numbers are. Also, the real scale is affected by a huge number of factors. The scale gets higher as the quality goes up, as it's easy to get very nice produce from a normal plant, while you're more likely to get the same quality of produce from plants of higher quality. Also, the type of seed determines the scale: Common seeds have a very small scale, while Special seeds have a rather large scale. Fertilizer also seems to play a role, as does the age of the plant (you're more likely to get higher quality produce from a plant that's been harvested a couple of times). And this is also a sliding scale, as it's entirely possible to get different qualities of produce from a single plant.
Did any of that make sense?