Look at the soil and the plants as one entity......The native plants all serve some type of purpose. We may not understand what it is but they weren't just randomly put here without rhyme or reason. If certain plants are trying to take over or become very persistent then its likely due to an issue with the soil. There's much more to soil than just what's on a soil test......
And that entity is part of a larger entity including he animals that eat the plants.
What is new or has changed over time. There may be many things, but one thing mentioned was a change in planting technique where a plow was replaced by herbicide. Let's set aside the significant negative impacts to the soil with a bottom plow and think about what it does. It turns the soil over which kills ALL existing plants. If you have deep highly fertile soil with very good levels of OM, the disruption to the soil may have a relatively small impact on its productivity. That impact does add up over time as the process is repeated, but in the best soil, the productivity may not decline enough to be of concern over your lifetime, especially if you offset natural nutrient cycling with high inputs of commercial fertilizer. On the other hand, if you have marginal soils, those negative impacts may be devastating and cascading over a short time.
So, what happens when the OP turns from the plow to herbicides for killing vegetation. We think of gly and a few other herbicides as "non-selective" or "broad-spectrum" and we tend to think they kill everything equally like a plow, but they don't. For example, some plants are naturally resistant to gly. For example, at 2qt/ac gly will kill some of the clover plants in your field, but others will recover. At 3 qt/ac you kill the majority of the clover but probably not all of it.
My next question becomes, how well did the OP do at using herbicides? What plants are taking over? I could not tell from the pictures, but someone suggested a sedge. Is a sedge controlled by gly? At what rate? Was the sprayer calibrated? After 5 years of planting RR beans and spraying multiple times with gly, is it possible that the weeds that survived the gly, because they were more resistant naturally than those that died, had more offspring and passed on that resistance?
It is a complex system, and one size does not fit all. Since I've converted my 2-bottom plow to a lawn ornament, I've had to learn a lot more about specific weeds. I've become more tolerant of weeds in general which has reduced my use of herbicides. At the same time I've become more focused on any weed that seems to becoming dominant in a field. It is becoming dominant most likely because I've removed the competition for it.
I'm just rambling and I have sympathy for the OP. I'm still going through something similar dealing with marestail. I'm switching to a Liberty generic for burn-down because of the how it controls my specific weed. I'll need to continually keep an eye out for other weeds becoming dominant in a field. I just hope the next weed that eventually becomes dominant is one that deer eat, love, and has good nutrition! (But then I guess it wouldn't really be a "weed" to a deer manager).
Thanks,
Jack