One obvious difference between the main plot and the subplot in King Lear is the fact that the main plot concerns two daughters (the third being absent), while the subplot concerns two sons. In both cases it is a question of a father's title and properties being taken over by his offspring. Shakespeare's theme is about old age and the way one generation inevitably and relentlessly replaces the generation that came before it. Shakespeare wanted two sons to balance the two daughters in order to show that his theme was macrocosmic and not microcosmic. In his play Measure for Measure, Shakespeare has Vincentio, the Duke of Vienna who is disguised as a friar, give the imprisoned Claudio some examples of the vanity of human existence, including the following regarding children:

Friend hast thou none;
For thine own bowels, which do call thee sire,
The mere effusion of thy proper loins,
Do curse the gout, serpigo, and the rheum,
For ending thee no sooner.

In other words, your own children wish you were dead so that they can inherit whatever property you have acquired and will free them of the burden, or possible burden, of taking care of you in your old age. We see plenty of examples of this in our own times because old people take up so much space and seem to enjoy pharmaceutical immortality. It is true enough that Goneril and Regan care nothing about their father King Lear and only want his property, and that Edmund only wants the title and property of his father Gloucester. Edmund expresses his thoughts on this subject in a letter which he attributes to his gullible brother Edgar.

'This policy and reverence of age makes the world bitter to the
best of our times; keeps our fortunes from us till our oldness
cannot relish them. I begin to find an idle and fond bondage in the
oppression of aged tyranny; who sways, not as it hath power, but as it is suffered. Come to me, that of this I may speak more. If our
father would sleep till I waked him, you should enjoy half his revenue forever, and live the beloved of your brother, Hum–conspiracy!—“Sleep till I waked him,—you should enjoy half his revenue,”
(Act 1, Scene 2)

Edmund follows up on the effect of the letter by telling his father:

"I have heard him oft maintain it to be fit that, sons at perfect age, and fathers declined, the father should be as ward to the son, and the son manage his revenue."

Regan expresses a similar idea in an exchange with her father in Act 2, Scene 4, when the two selfish daughters are stripping Lear of his provisio to keep a retinue of a hundred knights. When Lear pathetically protests, "I gave you all," Regan replies, "And in good time you gave it." She was doing him a favor to take it off his hands, since he was getting too old and senile to manage it himself. In fact, he held on to it too long to suit her. Her sister Goneril is in complete agreement. They have no gratitude for the gift of Lear's entire kingdom divided between them. They feel it is their property and that the old man was only obstructing them from enjoying possession by insisting on remaining alive. They would like him to die. 

In both the main plot and the subplot the elderly fathers find themselves cast out into the open country where they are subject to exposure and slow starvation. Gloucester has even been blinded. There is a touching scene in which the two old men, now worse off than beggars, come together by chance in an open field and commiserate on their fate. They have learned the bitter truth that there is little love in this world but that life is an ongoing struggle for existence. Lear tells Gloucester:

If thou wilt weep my fortunes, take my eyes.
I know thee well enough; thy name is Gloucester:
Thou must be patient; we came crying hither:
Thou know'st, the first time that we smell the air,
We wawl and cry.     (Act 4, Scene 6)

Cordelia, Edgar, and Kent, of course, are exceptions to the general rule and serve mainly as contrast to the ruthless, selfish Goneril, Regan, and Edmund. It is appropriate that Lear's two vicious daughters both fall in love with the Gloucester's villainous illegitimate son Edmund. "Birds of a feather flock together." Or, as Albany tells Goneril:

Wisdom and goodness to the vile seem vile:
Filths savor but themselves.     (Act 4, Scene 2)

So there are more similarities than differences between the main plot and the subplot. Both plots are intended to illustrate the same truth: that each generation (to use Keats' terminology in his "Ode to a Nightingale") is trodden down by the hungry generation it created and nourished. It can't be any other way.

Both the main and the subplot in King Lear take the relationship between a father and his children as the key theme. In both cases, there is a worthy, loyal, dependable child (Edgar/Cordelia) who is forced into exile because of a father too blind to see that he is being deceived by a silver-tongued sibling. Gloucester sends Edgar into the wilderness based on a ploy by Edmund, who leads Gloucester to believe that Edgar is a would-be usurper. Despite this, Edgar remains true to his father and never stops loving him, proving that he was truly loyal all along. Cordelia, meanwhile, is judged to be untrue by Lear because she will not flatter him. By comparison to her sisters' speeches, she comes off very poorly in Lear's eyes, and thus he disinherits her. In the end, however, both fathers have set their store by the wrong siblings: Edmund is seething with resentment towards his father and ultimately participates in his downfall, while Goneril and Regan begin working against their father at the first opportunity, as soon as Cordelia is out of the way.

Both fathers, through their own short-sightedness, make poor decisions because they have failed to see their children in a true light. This is symbolized through Gloucester's actual blindness in the play—he was blind before because he would not see, and thus he is made physically blind as a result of his poor decisions.

If we assume the main plot follows King Lear and his three daughters and the subplot follows the Earl of Gloucestor and his two sons, then there are indeed numerous similarities and several interesting differences between King Lear’s plot and subplot. For one, as far as we know, Lear’s three daughters, Goneril, Regan, and Cordelia, all have the same mother, whereas Gloucester had his son Edgar with his wife and his son Edmund out of wedlock. Another obvious difference is the fact that Lear’s children are women and Gloucester’s children are men. However, both Gloucester and Lear have children who betray and children who remain loyal to them.

Other similarities between the two older men include a distinct lack of judgment when it comes to the value of their offspring. Lear rewards Goneril’s and Regan’s flattery and punishes Cordelia’s honesty. Gloucester underestimates Edmund’s resentment towards his illegitimacy and falls for his slander of Edgar. Lear and Gloucester receive harsh punishments for their mistakes as fathers, but the two men eventually reconcile with their faithful children. One final difference is that there seems to be more hope for Gloucester than for Lear, who dies with Cordelia’s dead body in his arms. Gloucester dies happy after reuniting with Edgar, who lives on.