tomatoes are actually fairly low in nutrients compared to other fruits for sale in the store. they aren't bad for you, so there isn't any good reason to restrict tomato consumption, and i eat a fair amount of them myself, but i eat them with more nutritious fruits like red peppers, limes and avocados, and/or with high nutrient roots like beets or carrots and high-nutrient greens like kale and broccoli. tomatoes are better thought of as a low nutrient spice, like pepper or salt, whose primary purpose is to add flavour, than as a nutritious part of the meal. however, they aren't quite as useless as lettuce or cucumbers; they're in a middle category, with apples and peaches and pears, of fruits that you can do better than and should if you can, but shouldn't necessarily be actively avoided, if you like them. have a pear or an apple or a tomato if you like, but realize it has almost no nutritional value. if you don't want to do the research, just make sure you always have a red pepper and/or an avocado in any meal you eat with a tomato in it.

i would also suggest buying hydroponic tomatoes to maximize nutrients and to avoid organic tomatoes, as the pesticides that organic farmers use are more dangerous than the ones conventional farming uses. 

adding more carotenoids won't do much good. these are very poor sources of vitamin a (your body will convert them to retinol, but only if it has to, and at a much lower efficiency rate than previously thought. humans are in truth actually not very good at converting carotenoids, like beta-carotene and lycopene, into vitamin a. it is advised to seek true retinol, which is only found by eating meat, or consuming milk products, like cheese. i eat a lot of eggs, partially for that reason.) and there is no good science upholding any sort of benefit of lycopene, despite many attempts to find one in order to market tomatoes as healthy fruits. at best, lycopene is a very low potency form of vitamin a. lutein has a more established role to play in eye health, but you're still better off eating an avocado or a bell pepper, or a carrot.

tomatoes don't have much vitamin c and adding more would likely make them more citrusy. that would be a better addition, in my opinion. i'd like that, myself, but americans like sugar in ways that i don't. i prefer tarty citrus foods over sugary cakes and candy, but i'm a little weird. i would drink fresca or sprite when i was a kid by preference and choice, and not coke or pepsi, and i still prefer caffeinated mt dew to any cola, and dr pepper to coke. i used to get key lime or lemon or rhubarb pies for my birthday when i was a little kid, instead of chocolate cake, which i found made me bloated and sick. i preferred a good fruit filling - apple or cherry or rhubarb or lemon or lime - over chocolate filling or icing or sugar. i have always liked sour and have never really liked sweet. i'd get big turks instead of sugary chocolate bars. i'd prefer sour patch kids to smarties.

there are lots of sources of vitamin c in western diets and we don't really need more, but it would still be a better option than trying to cram more low potency vitamin a into the fruit, with little to no actual benefit to it.

i'm not opposed to genetically modifying food if there's a potential benefit to it, but i don't see any value in this, and will stick to the red ones. 

the tomato industry has been struggling for decades to market it's product as healthy because it's a fruit and it has this perception that people want tomatoes to be healthy because they're fruits. it should abandon this. tomatoes will sell as flavouring without the need to try to market them as healthy. it's enough for them to not be unhealthy - for them to be neutral - for them to be good flavouring agents.

https://www.ctvnews.ca/winnipeg/article/why-you-might-see-purple-tomatoes-at-the-grocery-store-next-year/