First, an apology. I guess I tend to live in a happy Catholic bubble sometimes. I honestly did not remember any great controversy surrounding Fr. Serra. After you brought it up, my dear old mother showed me this article from yesterday’s L.A. Times:
latimes.com/local/california/la-me-serra-20150117-story.html#page=1
Now the L.A. Times is usually no great friend of the Church, but even this article presents a more balanced view of Junipero Serra than you seem to acknowledge. I think lvcabbie in the previous post here and blog link has done as commendable and convincing a job as any in pointing out the revisionist tactics being used to discredit Serra.
Concerning Pope Francis’ love for the poor, I think it would be a mistake to think the Holy Father only cares about our temporal wellbeing. His first major publication, Evangelii Gaudium, The Joy of the Gospel, was all about evangelization - proclaiming the Gospel message in our world today. The main business of the Church is still winning souls for Christ, as it was in Serra’s time, even if the way we go about it has changed with the times.
I do not see the California Mission system as a means of enslavement, but as a support system for a people facing inevitable changes. Seen in that light, Fr. Serra cared for the poor and suffering just as much as Francis does now. I still see plenty of creditable evidence in support of Padre Serra, and apparently Pope Francis does too.