1/ Dorothea Brooke, Edward Casaubon, Will Ladislaw. Supporting characters: Celia Brooke, James Chettam, Mr and Mr Cadwallader, Mr Brooke, etc.
2/ Tertius Lydgate, Rosamond Vincy.
3/ Fred Vincy, Mary Garth. Supporting characters: the Vincys, the Garths, Camden Farebrother, Peter Featherstone, etc.
We can also mention the 4th plot of Nicholas Bulstrode and John Raffles.
Unlike the 2 strands in Daniel Deronda, these plots are not entirely separate from each other. E.g. plot 1 and plot 2 are connected by Will Ladislaw; plot 2 and 3 are connected because Fred is Rosamond's brother, Lydgate is friends with Mr Farebrother, and expectations regarding old Featherstone's will affect everything including Rosamond's marriage; plot 1 and 3 are glued by the relations between Mr Brooke and the Garths; plot 4 is linked to plot 2 through Lydgate (who is associated with Bulstrode), to plot 3 through Featherstone's legacy (which brings Rigg Featherstone to the area and then brings Raffles, who is Rigg's stepfather) and through Mrs Harriet Bulstrode née Vincy (wife of Mr Bulstrode, sister of Mr Vincy) and to plot 1 through Ladislaw (who is in some ways, I don't know what, related to Bulstrode and his shady past). In addition, there's always the politics in the background that connects or separates the characters and puts them into place, as Whigs or as Tories, etc.
The 3 main plots have 1 important thing in common: the process of learning and growth, of doing wrong things and realising the mistakes and becoming better. That refers to Dorothea, who marries the wrong man; Lydgate, who marries the wrong woman; and Fred, who has to work and improve himself to be accepted by the right woman.
I've written about Mr and Mrs Casaubon. Let's focus on the 2nd plot.
"... Those words of Lydgate's were like a sad milestone marking how far he had travelled from his old dreamland, in which Rosamond Vincy appeared to be that perfect piece of womanhood who would reverence her husband's mind after the fashion of an accomplished mermaid, using her comb and looking-glass and singing her song for the relaxation of his adored wisdom alone. He had begun to distinguish between that imagined adoration and the attraction towards a man's talent because it gives him prestige, and is like an order in his button-hole or an Honourable before his name.Think about Rosamond for a moment. She marries Lydgate, and this is what happens:
[...] Lydgate could only say, "Poor, poor darling!"—but he secretly wondered over the terrible tenacity of this mild creature. There was gathering within him an amazed sense of his powerlessness over Rosamond. His superior knowledge and mental force, instead of being, as he had imagined, a shrine to consult on all occasions, was simply set aside on every practical question. He had regarded Rosamond's cleverness as precisely of the receptive kind which became a woman. He was now beginning to find out what that cleverness was—what was the shape into which it had run as into a close network aloof and independent..."
"To Lydgate it seemed that he had been spending month after month in sacrificing more than half of his best intent and best power to his tenderness for Rosamond; bearing her little claims and interruptions without impatience, and, above all, bearing without betrayal of bitterness to look through less and less of interfering illusion at the blank unreflecting surface her mind presented to his ardour for the more impersonal ends of his profession and his scientific study, an ardour which he had fancied that the ideal wife must somehow worship as sublime, though not in the least knowing why. But his endurance was mingled with a self-discontent which, if we know how to be candid, we shall confess to make more than half our bitterness under grievances, wife or husband included. It always remains true that if we had been greater, circumstance would have been less strong against us. Lydgate was aware that his concessions to Rosamond were often little more than the lapse of slackening resolution, the creeping paralysis apt to seize an enthusiasm which is out of adjustment to a constant portion of our lives. And on Lydgate's enthusiasm there was constantly pressing not a simple weight of sorrow, but the biting presence of a petty degrading care, such as casts the blight of irony over all higher effort..."The interesting bit is that, after Middlemarch, she throws away everything else but keeps Rosamond Vincy, renames her, changes very little about her character and personality- even the fondness for music and horse-riding is retained; it's only the family and the circumstances that are different. It seems that, after writing a novel about the development of Dorothea, George Eliot turns her interest to Rosamond and wants to see what happens to a spoilt, selfish, frivolous, shallow, vain and extravagant girl like her when she, instead of finding someone who yields to her wishes, meets someone who can manage her, tame her, dominate and control her. In other words, she places the same character in different circumstances. Thus we get Gwendolen Harleth and the novel Daniel Deronda.