Empress Matilda and Eleanor of Brittany both were the right heirs to England, and both were passed over in favor of male claimants. Matilda at least had some support and fought a war for it, but Eleanor was pretty much acknowledged as the legal heir, but then tossed in prison and ignored for her entire life.
400 years later, with the disputed succession between Jane and Mary, there was again a bit of conflict, but this time fighting for the rival rights of two female claimants. Mary was then installed, and was followed by her extremely successful sister.
Obviously 400 years is a tremendous amount of time, but still it begs the question in my mind, were there any specific changes in politics or cultural norms that allowed the nobility of the 16th century to be firmly behind a female monarch, while those in the 12th century basically gave a sympathetic nod and preferred to back a usurper they didn't even like?
Most of the factors that lead to a Queen Mary's ascension were contingent circumstances in the mid-sixteenth century. There are probably some long term structural causes that may have made a female monarch more appealing in the sixteenth century, but the local and immediate circumstances overruled them.
The first element is that there was no legitimate or illegitimate male heir to succeed Edward. Henry VIII's bastard son Henry Fitzroy died in 1536, and was the only other son of Henry VIII. The remaining surviving heirs after Edward VI were Mary Tudor, Elizabeth Tudor, and then the Queen of Scotland, Mary Stuart. Lady Jane Gray was the granddaughter of the younger daughter of Henry VII, and she inherited this status from her mother, not her father, Henry Duke of Suffolk. So, the first reason was simply that there was no male heir to choose from in the Tudor dynasty (Which, despite its contentious beginnings, was far more settled in 1553 than in 1485).
The next element was during the end of the reign of Edward, the main political figure exercising power was John Dudley, Duke of Northumberland. After seizing power in 1550, and appointed as Lord President of the King's Council, Northumberland was the most powerful political player, perhaps even including the 13 year old king Edward. Northumberland was a hated and feared Lord President, both by conservatives at Court, and by the populace at large. During the last two years of Edwards life, Northumberland seemed to be encouraging more unpopular religious reforms r, including a further revised Prayer Book in English, a more explicit denial of transubstantiation, and forbidding any prayers for the dead. Before Archbishop Cranmer could implement the reforms, Edward's health declined to the point that the settlement of succession took priority over reforms.
Now, Northumberland and Edward VI wanted to prevent the ascension of Catholic Queen Mary. Rather than promoting Elizabeth, whose religion was known but her political alliances weren't, Northumberland and Edward chose to try and promote Lady Jane, the next closest heir, a known protestant, and Northumberland's daughter-in-law. Lady Jane was proclaimed in London, but only "reigned" for about ten days. The reason was because the more proper heir, by Henry VIII's will and by question of succession, Mary Tudor rose to the occasion, and the people rose with her.
So, why Mary Tudor? The first aspect was that she was notoriously popular with conservatives at court, and the populace at large. Mary was a Catholic who had formally submitted to Edward, but was known to be a member of the faith. The majority of Englishmen and women had born and suffered under the religious reforms of Edward, Somerset and Northumberland. They had accepted them either due to the natural deference to authority that permeated Tudor society (in the case of the Eucharist and Chantryies) or because their attachment did not run deep enough to stir the people to action (as with the dissolution of most of the monasteries). However, most of the people did not want the reforms, in fact they shattered aspects of communal life in a way that did stir the people to rebellion in 1536 and 1549. In Mary, the people had a champion - a monarch who they could trust would return them to the true Catholic religion. Elizabeth was of a reformed type, and Jane had the downsides of being both evangelical and a known pawn of the hated Northumberland.
Rather than risk the crown falling to one of the reformed women, to a Scottish female child (11 years old vs. Mary Tudor at 37), the people outside of London did cheer and rise for Mary. There was no real military conflict, but Mary had the support of conservative elites in East Anglia and the midlands, and they rallied to her cause. Brigden describes the news that arrived at the Tower of London, where Northumberland and Jane were as "country folk flocked to their rightful queen...protested against Lady Jane's proclamation...mariners mutinied against their captains, and tenants refused to rise with their Lords for Jane." With the grim reality setting in, and a veritable army marching on London, Jane and Northumberland surrendered. Mary was proclaimed queen to extreme fanfare.
After all these events, I would recommend reading the recent essay by Cynthia Herrup "The Kings Two Genders" (Journal of British Studies, July 2006). Herrup explains how Mary and Elizabeth used the language of kingship to describe the way they ruled, and how they derived authority. Many of the quotes she uses are well know - Elizabeth having the heart and stomach of a King is one - but she presents the information in a new way that helps explain how these two women managed to explain monarchical authority in a way that made the people accept masculine (perhaps even patriarchal) power emanating from a feminine body.