Growing in pots one has to use potting soil. Hopefully you are using bagged potting soil. Don't fertilize until planted in 4" pots. Fertilizer helping them grow when they are unable to make enough food for themselves causes plants to elongate and thin leaves in an effort to reach more light.
Have you used fertilizer? That might also be why they are so elongated. I usually up pot into a 4" first, allow roots to fill and make sure the starts are used to the amount of light, wind before planting in the prepared beds of the garden. Harvest the broccoli in a timely fashion and finally, conduct regular inspections of the lower leaves and stems. Add some nitrogen to the soil, if appropriate. If your broccoli plant is turning yellow, ensure the soil is of the proper pH. I also rip that thin fabric off, or cut it off before transplanting. Limit the spread and retain what harvest you still can. What are the night time temps? Good time to start if you want to transplant in your garden. If you have a covered patio or deck I would definitely put them out of doors. Lots of answers about that as well on our site. Acclimating thickens the epidermis to protect the other cells from the radiation of the sun. If your plants have never been in the sun you will have to acclimate your starts to the sun before they ever feel sunlight on their leaves. As long as the temp is below 90 degrees F plants will do just fine. We've got lots of info on lighting on our site. Those seedlings will strengthen if you get a real grow light. You need to get a real grow light to start plants indoors.
If they are indoors by a window that is just not enough for light. Are you indoors? A greenhouse? No they aren't ready to be transplanted.
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